The fungicide chlorothalonil is considered to be non-selective and used commonly to control a broad spectrum of plant diseases. Effects of Chlorothalonil on soil microbial community were investigated at recommended rates by Biolog-Eco detecting method. The results showed AWCD values of treatment were all lower than untreatment in three soil layers. At the initial stage, AWCD values of all treatments were lower than the control, and its changing trends were different between surface, upper layers and under layers. The trendency was similar showing increased during two months and decreased till tweleve months in upper and under layer control soil after chlorothalonil application. For upper and under layer treated soil, the trend indicated decreased during two months, then increased at the period of 2-4 months, finally decreased till 12 months. Principle component analysis facilitied for average optical density in different layers of soil microbial community while largely carbon sources had similar loadings before spraying and two months later. The ability of single carbon conversion ratio of soil microbial community obviously improved after chlorothalonil spraying. chlorothalonil residue in soil was determined accompanying with time after chlorothalonil treatment.The fluctuation tendency was all declined accompanying with times after spraying chlorothalonil.In conclusion, chlorothalonil has effects on soil microbial community of Larix artificial forest.