[Background] Tetracycline antibiotics (TCs) are a broad-spectrum antibiotic, widely used in livestock and poultry breeding. The residue of tetracycline antibiotics in animal manure may cause changes of soil microbial community. [Methods] On the basis of the investigation and analysis of TCs pollution in the soil of main vegetable bases and the livestock manure of major large-scale farms in Chongqing, China, the effects of tetracycline antibiotics on the structure and diversity of soil microbial community were investigated by high-throughput sequencing. [Results] The TCs content in soil was increased by applying livestock manure. The contents of TC, OTC and CTC in the soil under pig manure treatment were 171.07-660.20 μg·kg-1, 25.38-345.78 μg·kg-1 and 170.77-707.47 μg·kg-1, respectively. The contents of TC, OTC and CTC in the soil under the treatment of chicken manure were 166.62-353.61 μg·kg-1, 122.25-251.23 μg·kg-1 and 15.12-80.91 μg·kg-1 respectively. The content of tetracycline antibiotics (TCs) in edible parts of Brassica juncea var. gemmifera was increased after livestock manure treatment, among which pig manure had the greatest influence on the increase of TCs content, and the larger the dosage of pig manure was, the more significant the increase of TCs content was. Proteobacteria, Acidobacteria, Actinobacteria, Chioroflexi and bacteroidetes under livestock manure treatment were the dominant phyla, accounting for 85.2%-92.4% of the total abundance of soil bacteria. [Conclusions] The soil OTUs under the treatment of pig manure was higher than that under the treatment of chicken manure. Biogas residue after fermentation treatment can effectively reduce the environmental and ecological risks caused by antibiotic residues.