Abstract: This paper investigated the effects of crop planting structure on agricultural output value and non-point source pollution by analysising the relation of crop diversity, agricultural output value, and released pollutants. The panel data of 30 provinces in China from 1990 to 2016 were included. The results showed that crop diversity had an inverted u-shape effect on agricultural output value and there were greatly diversified crop categories for non-dominant crops (relatively weak comparative advantage) currently, which had an inhibitory effect on agricultural output value and had a positive effect on agricultural non-point source pollution. Holding all other things constant, a 1 increase of the crop diversity will lead to a decrease in agricultural output value of 1.5% and an increase in agricultural non-point source pollution of 1.3%, respectively. The increase of regional dominant crop diversity had a greater inhibitory effect on agricultural non-point source pollution, when the crop diversity rises 1, agricultural non-point source pollution decreases 1.5 percent. Besides, the crop diversity had a negative effect on comprehensive indicators of output value and pollution. With the outflowing of agricultural labor, reducing crop diversity benefits agricultural output value; the increase of crop diversity is beneficial to the growth of agricultural output value when natural ecosystems are fragile. In order to improve agricultural income and enhance ecological environment, the crop varieties and planting areas should be reduced for those weaker comparative crops, meanwhile developing agricultural products, local agricultural products, and building agricultural brands will substantially help. For other factors we discussed, agricultural infrastructure, farmers’ awareness of disaster prevention are significantly affecting the agricultural outputs and need be addressed properly.