Abstract: To investigate the relative abundance of microorganisms, analysis distribution and enrichment of pathogenic microorganisms and antibiotic resistance genes in piled manure and surrounding soil, 3 piled manure and 3 surrounding soil specimens were collected in dairy farm in Ningxia. The DNA samples were exam based on metagenomic sequencing; Contigs were estimated by taxonomy annotation using NCBI-NR database; PHI database was used to detect abundance of pathogens and virulence genes; ARDB database was used to detect abundance of antibiotic resistance genes（ARGs）. The results show that 39 phyla, 76 classes, 167 orders, 369 families, 1 103 genera and 3 264 species were obtained in 6 samples. Bacteria absolute superiority and accounted for 97.49% and 98.63% in piled manure and soil samples, respectively. The microbial communitys in dairy farms are mainly composed of 39 phylum such as Proteobacteria, Bacteroidetes and Actinomycetes. RAs of pathogenic microorganisms and virulence genes in manure was higher than in soil（657 961.00±391 617.24: 155 553.67±43 038.27, P＜0.01）. There was no difference in the RAs of pathogens and virulence genes at different soil depths, while the RAs of 34 pathogens in the manure increased with the increase of the piled depth. The dominant species including Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Streptococcus pneumoniae, Edwardsiella ictaluri, Magnaporthe oryzae and Xanthomonas oryzae. Total of 78 dominant ARGs root in 49 antibiotics（RAs＞0.5%） were observed in piled manure, which were higher than 49 ARGs root in 31 antibiotics in the soil. Among them, the RAs of 29 ARGs were increased with the piled depth. It mainly includes streptomycin A（vatb）, lincomycin/macrolide antibiotic/streptomycin B（tlrc, cara, oleb, srmb）, vancomycin（vanug）. Waste manure piled in dairy farm will promote the accumulation of pathogens, virulence genes, ARGs, and may cause pollution to the surrounding soil.