In both the DC and Marvel comic universes, evil is a universal constant. No matter how many times the heroes take down a bad guy they seem to return more powerful than ever. In the DC Universe, one of worst evils in the galaxy is Darkseid, the ruler and god of Apokolips. He is evil incarnate, literally feeding off the misery and pain of others to increase his already formidable powers. He has brought an entire worlds down to their knees and not broken a sweat. The Marvel Universe has the genius and pragmatic Thanos, the lover of death and master of destruction.
With the Infinity Gauntlet in his hand he is undefeatable, none of Earth's Mightiest Heroes can even hope to challenge him. He is cunning, cruel, deceptive, and intelligent beyond belief. He does not even see himself as evil or wrong as he has risen above all such labels. As audiences saw in Avengers: Infinity War and Avengers: Endgame, Thanos is quite possibly the greatest threat to peace in the entire universe. Both of these villains are universal level threats in their respective universes and ensure that the heroes who face them will suffer nothing but pain.
Darkseid
The dark god Darkseid, is legendary amongst DC and comic book fans in general. Whenever or wherever he appears death, chaos, destruction, and despair follow behind him like a shadow. No matter which version one researches, his origin is filled with blood and mayhem. He is one the New Gods and is in a constant state of war with the benevolent gods on New Genesis. In actuality he is at war with life itself as he is often searching for the Anti-Life Equation. He will stop at no ends to find this power, destroying any and all that stand in his way.
The power of the Anti-Life Equation allows one to have complete domination over the will of any given race or species. His power level is quite high as he can go toe to toe with Superman and his true form is the size of a star. Also, he has various abilities based on his Omega powers. Due to his godhood, he is a multi-dimensional being that takes on avatars in order to reside in any given universe. On numerous occasions he has been dubbed a multiversal level threat.
Thanos
Known around the galaxy as the Mad Titan, Thanos has annihilated many races and civilizations around the universe. Since he was a young child, he has had a perverse fascination with Death. This eventually morphed into an obsession as he has committed atrocious acts in order to gain what he perceives as her "love". He gathered an army of cruel, murderous people that follow his every desire. He has searched the cosmos for any item or weapon to cause death on a massive scale. He originally was content with the power of the Cosmic Cube and its reality altering abilities.
As time went one he discovered the infinity stones and constructed a gauntlet to use all of them at once. He gained the power of a god and with a single snap of his fingers, he wiped out half of all life in the universe. Aside from his use of powerful items, he is one of the greatest minds in the Marvel universe. He can outwit those with cosmic omniscience and even talk them into joining him. Thanos has managed to destroy and rebuild the universe more times than he could have ever imagined. During one adventure, he fought a future version of himself and found him lacking.
The Battle
Many fans have wondered and debated about who would win an in all-out nothing held back battle between Darkseid and Thanos. If they were to engage in a fight then it would have to be somewhere mostly empty as the fallout would kill anyone near them. Neither of them would care much about innocents and would probably just battle it out wherever they felt like. Darkseid, if using his common avatar, would be very similar to Thanos in both height and build. Without either the Cosmic Cube or the Infinity Gauntlet, Thanos would immediately be at a disadvantage.
He would quickly realize that physical blows do very little to damage Darkseid unless then are filled with some kind of energy. Luckily, Thanos's greatest weapon is his mind and even Darkseid cannot top his intellect. If he could devise some kind of strategy to strike Darkseid where it hurts then he would be able to subdue him for a time. However Darkseid would not be caught off guard twice, it is doubtful that Thanos would have something on hand to kill him so he could mount a counterattack. If Darkseid used even two or three of his Omega powers then Thanos would be in a world of trouble.
The Victor
Thanos has the very rare ability to use his wits to defeat even a god level adversary. His words are weapons and he can use them with masterful precision. Against Darkseid though, words would not get him very far. The fact that even provided a challenge to the dark god would make him want to vanquish Thanos quickly. Both men have giant egos and when they get scarred, all hell breaks loose. Darkseid would see Thanos as a large enough threat to warrant him not holding back. If he employs all of his Omega powers then Thanos would not stand a chance. While he would put up a good fight, Thanos just cannot match the raw and violent powers that Darkseid contains within himself. Darkseid is essentially Anti-Life itself and he would be more than happy to send Thanos to his beloved Death for eternity.