Based on the panel data of 31 provinces in China from 2004 to 2013, this article utilized dynamic panel model and differential GMM estimation and chose chemical oxygen demand (COD) and ammonia nitrogen (AN) to be the organic and inorganic pollutant indicators. It did empirical research on China's water environment pollution discharge induced by the structure effect of trade openness. The research results show that the scale and technical effects of economic growth are the main effects influencing on water environment pollution discharge, and the direct structure effects of economic growth influencing on water environment pollution discharge is not significant. The structure effect of trade openness aggravates China's water environment pollution discharge to a certain extent. By leading in relevant cross terms of trade openness, we can distinguish the source of comparative advantage determining structure effects of trade openness. It is found that there exist no pollution heaven effect and factor endowment effect on China's water environment pollution. The structure effect of trade openness can lead to lower water pollution discharge in western part that is less developed, but can increase the water pollution discharge in the mid-eastern China.