In more than forty years of open and reform, China is experiencing the largest and fastest urbanization in the world. Urbanization not only brings economic growth and efficiency improvement, but also aggravates the unfair distribution of social resources. This paper constructs the indexes of urbanization, distributive justice and economic efficiency with factor analysis method, and employs the VAR model and the membership function to construct the coordination degree model of three systems. Taking the data of Shanghai and Chongqing as examples, the paper compares and analyzes the coordination degrees between the two cities. The conclusions are as follows: 1) The urbanization indexes and economic efficiency indexes of Shanghai and Chongqing from 1997 to 2017 are on a rise trend, but Shanghai’s distributive justice index shows a big "V" shape, while Chongqing’s distribution justice index shows a linear downward trend. 2) The coordination degrees of two or three systems of urbanization, distributive justice and economic efficiency in Shanghai and Chongqing are in a state of coordination or basic coordination. The coordination degree of urbanization and distributive justice, the coordination degree of urbanization and economic efficiency, and the coordination degree of three systems in Shanghai are higher than those in Chongqing. 3) The results show that the fluctuation trend of coordination among the systems of urbanization, distribution justice and economic efficiency in Shanghai and Chongqing is consistent. The fluctuation of coordination in Shanghai is mainly affected by economic efficiency index, while that of Chongqing is mainly affected by distribution justice index. According to the research conclusion, the paper puts forward relevant policy suggestions.