Hi!
Would you tell me which is the correct one.
a) There is a [color=red]great population in Tokyo.
b) There is a [color=red]large population in Tokyo.
My choice is b, large but I don’t know why is it large is the right one.
I agree with your choice, alv, and as a contributor to this large population I have to say it’s not great but only large. 
It seems to me that to say ‘a large population’ is much more natural and popular than to say ‘a great population’. Maybe the combination of those two words isn’t so great. 
The collocation “large population” is natural.
“Great population” would be used in this way:
“The great population growth/explosion of the 60’s, was…”, and that collocation is “great growth/explosion”.