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I dont know if thanos can keep up with this one, but yes it is the same Emperor from the Warhammer 40k Universe.

Man Horus trounced him easily even though he died because of it. . Hell even current Abadon would beat the Emperor back in his prime.

Thanos would win imo.

Remember Horus was getting power from the 4 allmighty Chaos Gods and even then he was no match for him, he was holding back because he sensed that horus ''his son'' was still somewhere in there, when he was mortally wounded and horus killed his personal guard with the blink of an eye he understood there was no way to bring him back and launched the psychic power into him, still just before he shattered Horus soul he sensed the Chaos corruption fleeing from him and for a sec he sensed his son's soul.

Remember the Emperor attacks both your phisical and your soul, if he gets thanos soul then i think the game is over tho.