Returning livestock manure to the cropland as organic fertilizer is a sustainable and environmentally friendly treatment method, but its application also alters the soil microenvironment. However, the impact of soil microbial community disturbance and pollutant accumulation from different types of organic fertilizers remains largely unknown in South China. To fill this gap, we investigated the effects of organic fertilizers, including chicken manure, pig manure and vermicompost on the soil bacterial and fungal communities and environmental risks. The results show that applying organic fertilizer effectively increases the soil nutrient content. High-throughput sequencing of bacteria and fungi showed that the application of different organic fertilizers had differential effects on microbial community structure, with the highest number of microbe-specific OTUs in the vermicomposting treatment. Additionally, this study found no risk of heavy metal (Cu, Zn, Pb, Cr and Cd) contamination from short-term organic fertilizer application, but there was a risk of antibiotic (ENR and CHL) contamination. Functional microorganisms regulating heavy metals and antibiotics were identified by RDA analysis. This study facilitates the screening of types of organic fertilizers that can be safely returned to the field as well as developing strategies to regulate functional microbes.