In recent years, with the rapid development of science and technology, the construction of smart city has entered a new climax. But at the same time, due to the construction of smart city is still in the initial stage, there is no unified standard at home and abroad, so that the specific implementation process often leaves deficiencies, such as the more prominent problem of urban water pollution control efficiency. However, the research on this aspect is still blank in China. Therefore, this paper puts forward an empirical study on the impact of environmental protection technology investment based on smart city construction on urban water pollution control efficiency. This paper studies the core concepts of smart city construction and urban water pollution control. In order to improve the efficiency of water pollution control, we must establish a set of objective and scientific evaluation index system and matching efficiency calculation method. Therefore, this paper innovatively puts forward the empirical method of investment efficiency of environmental protection science and technology for water pollution control in smart city. Based on the current situation of smart city construction, this method classifies the factors that affect the efficiency of water pollution control, and optimizes the calculation method of empirical model. The optimized empirical model can be applied to smart cities with various economic structures, and is not limited by the size of the city, which can maximize the applicability of the model. In order to verify the actual effect of the empirical method, this paper takes Chongqing as the test object, and collects the data of the city in recent five years as the experimental sample. Through the analysis of the results of empirical tests, it can be seen that the test method of water pollution control efficiency in this paper has high accuracy, and can play an important role in water pollution control of smart city construction.