Excessively rapid rise of housing price brought by excessive prosperity of real estate market can affect factor flowing and enterprise behavior, and further aggravate the dislocation of resources, which is not conducive to industrial structure optimization. The property tax is expected to be an important policy to restrain the rapid rise of housing prices and to alleviate the resources dislocation by the declining of regionally relative housing price and to boost regional industrial structure optimization by the two paths such as industrial transfer and enterprise innovation. This paper uses the synthetic control method to evaluate the impact of the property tax policy on the optimization and upgrading of the regional industrial structure on the basis of theoretical mechanism analysis, and the research results show that Chongqing’s real estate tax policy has effectively restrained the rapid rise of housing price and significantly improved its industrial structure rationalization and advanced innovation level, and generally promoted the optimization and upgrading of the regional industrial structure and has obvious industrial structure optimization effect; Shanghai’s real estate tax policy is not significant to restrain the rise of housing price, high housing price obstructs the inflow of hi-tech talents, causes the upgrading of industrial structure to more depend on the development of low-level service industry, which is not helpful to regional industrial structure rationalization and which is not effective to promote regional industrial structure optimization as a whole. The difference in the effect of the real estate tax policy between Shanghai and Chongqing is not only from the implementation degree of the policy but also is because of the difference in regional economic development level and industrial structure. Real estate tax policy must effectively restrain the rapid rise of housing price and can better bring industrial structure optimization into fully play by combining local economic development reality.