Population migration has significantly impacted on Chinese governmental fiscal relation.Transfer payment serves as a policy tool in solving these issues on non equalization.Both authors of this paper tested from the empirical analysis and showed that，population migration has changed per capita transfer payment based on permanent residents in all areas via“denominator effect”.As far as the population shifts from the undeveloped regions to the developed ones，as a matter of fact that population migration has contributed to remission of non equalization resulted from transfer payment through numbering effect，which results from the incompleteness of transfer payment itself.It is necessary for the local government to improve the management of population and transfer payment system in order to break this deadlock.