With the enhancement of environmental policies and farmers’ consciousness of environmental protection, deep- litter pig rearing technology has gradually accepted by farmers. However, difficulties in reuse of deep-litter restricted the extensive application of the pig rearing technology. In this study, two types of deep-litters were used to produce organic fertilizer with high-temperature composting (FOF and ROF). The total nutrient content (N, P and K) was higher than 50 g/kg. The contents of heavy metals and Escherichia coli did not exceed the standard. Mortality rate of ascaris egg was higher than 95%. All indexes conform to the standard of commercial organic fertilizer. Pepper yield in the treatment with deep-litter organic fertilizer was comparable to those with chemical fertilizer (CF) and conventional organic fertilizer (POF). The results of PCR-DGGE showed that bacteria diversity in the five treated soils could be classified into three clusters. Soil bacterial communities of CF and control belonged to the same cluster, while POF was in the second cluster. The soil bacterial communities of FOF and ROF were in the third cluster. Fertilization could affect soil microbial diversity. The application of organic fertilizers could alter soil bacterial communities, while the application of CF had little effect on soil bacterial communities. Organic fertilizers produced from various sources had different effects on soil bacterial communities, and those with similar origin had similar effect on soil bacterial communities.