In the past 40 years after China adopted the reform and open-up policy, China’s expediting industries spatial agglomeration has resulted in severe damage to the environment. In China, the one whether the pollution haven hypothesis (PHH) is true or not is the hot issue under the research of academic circles. By establishing the mechanism model of industries spatial agglomeration and environmental pollution in this paper, we discovered upon our empirical study that China’s industrial spatial agglomeration process had apparent threshold characteristics for environmental pollution, those direct investment and scientific innovation of foreign merchants apparently improved environmental pollution, so PHH is not true in China and such conclusion provides empirical support for China’s industrial agglomeration and environmental policymaking. At the end of the paper, the policy proposals for improving environmental pollution in future are made, which have important significance for China’s high-quality economic development.