Abstract: Agricultural ecosystem is a half-artificial and half-natural complex ecosystem, which is greatly impacted by human activities. Many agricultural ecosystem problems appeared with the promotion and application of channelization farmland water conservancy construction in China. By the methods of field investigation, field experiment and laboratory analysis, studies were conducted from three aspects including effect of the distance to the channel (far, middle, near) on soil available nutrients, effect of different types of channel on water nutrient content and biodiversity of different types of channel. The results showed that (1) soil ammonium nitrogen and nitrate nitrogen showed seasonal variations with the same feature, which was higher in summer and lower in winter, the change of available phosphorus content showed no regularity; the content of soil ammonium nitrogen and nitrate nitrogen in different distance showed the rule of middle＞ far≈ near and far＜middle＜near, respectively; (2) morphological structure of channel had significant effect on the biodiversity, and the biodiversity of animal and plant species showed edaphic channel＞ concrete channel, the edaphic channel had little influence on the habitat and better function of biologic channel which was benefit for the matter and energy flow in agroecological ecosystem; (3) the purifying capacity of edaphic channel was higher than that of concrete channel, by monitoring analysis of pollutant content, the intercept purification effect of edaphic channel was better than that of concrete channel.