The population of A city is more than two times as many as B city’s. +200%/>200%
2) The population of A city is two times more than B city. 200%
A city has a population two times more than B city. 200%

As a native speaker, I wouldn’t use any of those options. I would say something like:
The population of city A is twice/double that of city B
City A has twice/double the population of city B

“Two times more” is unclear, since some people use it to mean “two times” (2x) but “two times more” implies that it’s the original amount plus an extra two times (x + 2x).