In order to study the influence of inoculated strains on composting microbial community structure, composting experience was conducted, which used the cow dung and straw as raw materials. Designing two groups, one was the group which added to fungi strains (code name: FLD, which were composed of three kinds of strains, and sequencing showed that Trichodermaviride, Trametes gallica and P.chrysosporium) in the secondary fermentation, the other was control group. Variation of microbial communities in inoculation and natural composts was studied with the PCR-DGGE technology. Results indicated that: The DGGE graphs showed a wave-like carve: up-down-up about the population. And the inoculated strains colonized successfully in the secondary fermentation of compost, they became the superior strains in the high temperature phase the strength of bands reduced in the cooling and maturation phases. The inoculation could increase the total count of fungi, enhance microbial diversity and accelerate microbial succession, then shorten the maturation phase.