The clipping from a clipper might be scaring him. If you're using the latter try scissors instead. You might also have hurt him in the past with one or the other. If so, consider a switch to scissors from clipper or vice versa to see if the new method makes any difference.
In case you're not doing so already, nails (like hair) are more flexible and thus easier to cut when wet so be sure to cut nails shortly after a bath.
Likewise, try showing him you doing it to yourself if you haven't done so already. Sit him on your lap while you do yours. This'll drive the point that others including yourself do it too, and should reassure him that it's safe in case he feels nervous about it.
Speaking of position, see if a new one might make a difference: with him on your lap facing the same direction as you do, the same with him facing you, at his side, in front of him.
Lastly, are you sure you're not hurting him? If not and you usually cut them very short, try leaving the nails a little bit longer. Also, a clipper flattens the nail somewhat if you cut the entire thing in one go, which can be scary and potentially painful, so try clipping in more steps instead.