The MC has been sharpening his skills for thousand of years. I think it is a post calamatic world, fighting against God's. I didn't read the novel, just saw the summary somewhere but now that I want to read it. I forgot the title.
better add more details that you can remember (or half remember) sounds like a few different things as is
Maybe he lived for 1000 lives and not 1000 years? The story should definitely be similar to what you are looking for even if its not the same. Record of a Thousand Lives Otherwise its most likely Everyone Else is a Returnee. It's just that I don't remember being any final boss in the description.