This paper studies the influence mechanism of industrial agglomeration and foreign direct investment (FDI) on green total factor productivity (GTFP). We use the SBM Directional Distance Function to measure the GTFP of Chongqing's manufacturing industry from 1999 to 2015. The results show that the level of GTFP in Chongqing's manufacturing industry is relatively low, which is contrary to the current green development mode. By clarifying the conduction path of industrial agglomeration and FDI on GTFP, we use the panel Tobit model to study the effect of industrial agglomeration and FDI on GTFP. The main findings are: the higher the level of industrial agglomeration, the more beneficial it is to increase GTFP. FDI has an inhibitory effect on GTFP. The spillover effect of FDI on GTFP is not significant. At the same time, FDI counteracts the role of industrial agglomeration in promoting GTFP. The findings in a present study indicate that, according to Chongqing's experience, the "pollution haven" is established. Therefore, relying solely on foreign technology to promote the development of the manufacturing industry has many drawbacks clearly. Only by improving the ability of independent innovation is the reliable way to enhance GTFP effectively.