IIRC......
Apocalypse = 1st Human Mutant, Extremely Powerful, but still Human.
Thanos = Mutant Eternal, Eternals are essentially Genetically Engineered Super Humans created by the Celestials to be Demi-Gods themselves, and are like Mutant's on Steroids with Strength/Endurance/Invulnerability on the level of Hulk combined with things like Flight, Speed, Mental Powers, Energy Blasts, etc etc.
It would be an interesting fight but unless Apoc has some type of Damage Absorption / Regeneration powers along the lines of Vulcan or Wolverine in his list of abilities, then he's going to loose by eventually taking a direct hit.