The effects of successive chlorothalonil applications at a rate 5 mg/kg and 25 mg/kg on residues of chlorothalonil and the diversity of soil microbial communities were investigated in red soil and Wushan soil. After four successive applications at 7 day cycle, the residues of red soil were higher than that of Wushan soil. Biolog-Eco plate detecting showed that, in red soil, the AWCD of CK was less than that of 5 mg/kg treatments, and significantly higher than that of 25 mg/kg treatments (P<0.05). In Wushan soil, the AWCD of CK was significantly higher than that of 5 mg/kg treatments and 25 mg/kg treatments (P<0.05). Principal component analysis of 31 carbon sources showed that the ability of single carbon conversion ratio of soil microbial community was also affected by chlorothalonil in different degree and there were significant differences between two types of soil.