It is of practical significance to study how to fully play the promoting effect of Shanghai Free Trade Zone (SFTZ) on China’s marketization of interest rate after setting up SFTZ. In terms of interest parity theory, this article tries to divide the process of China’s marketization of interest rate into different stages and conduct in-depth study of the formation mechanism of interest rate of each stage from the perspective of capital flow. The results show that marketization of interest rate is a system project. It can be divided into three stages: official interest rate supplemented market, two-track system and integration, according to the progress of marketization of interest rate, and the formation mechanism of interest rate of each stage varies. Free trade zone is a domestic and international hub for capital flow. The condition of capital flow influences capital supply, thus affecting the formation mechanism of interest rate domestically in free trade zone and promoting the progress of China’s marketization of interest rate. Marketization of interest rate, capital account liberalization, internationalization of RMB, and construction of international financial center are the supplementary, inseparable and transitional process. Therefore, the promoting effect of SFTZ on the marketization of interest rate, the capital account liberalization, the internationalization of RMB and the construction of international financial center should be made full use of. Finally, on the basis of it, this study explores hardships that China’s marketization of interest rate faces after the foundation of SFTZ and puts forward corresponding policy suggestion.