Based on the panel data of 288 prefecture level cities in China from 2000 to 2016, this paper uses DID and PSM-DID models to measure the net effect of RSCC on TUIS. The results show that: (1) RSCC failed to promote industrial structure rationalization (ISR) and industrial structure advancement (ISA), and failed to promote TUIS. (2) There is a time lag in the initial stage of RSCC implementation, and then RSCC has a negative and then positive impact on ISA and the inhibitory effect on ISR is gradually increased. (3) There are human capital crowding out, savings restraining, government expenditure and fixed assets investment not fully playing a role in RSCC. Although RSCC has a positive impact on regional development level and foreign direct investment, due to institutional mechanisms, TUIS has not been promoted. (4) RSCC significantly promoted ISR before 2012, and significantly promoted ISA after 2012.The effect of “two comparison” samples on TUIS is better than that of the whole, and there is no significant difference between the two groups. RSCC has no significant effect on TUIS of high-grade cities, but has a restraining effect on ISR of general grade cities. Therefore, we should better allocate the natural endowments and resources, strengthen the endogenous growth ability of the industry, and promote TUIS in the central region.