Manure application is a common practice that not only adds nutrients and organic matter to arable soils for crop growth, but also introduces antibiotic resistance genes (ARGs), posing a potential risk to human health. To investigate the mechanisms underlying the spread of ARGs in manured soil, especially the impact of manure-borne and indigenous soil microorganisms, a microcosm experiment with four specially designed treatments over a period of two months was conducted, including soil, soil with irradiated pig manure, irradiated soil with pig manure, and soil with pig manure. A total of 240 unique ARGs were detected via a high-throughput quantitative PCR (HT-qPCR) targeting almost all major classes of ARGs. Manure application significantly increased the diversity and abundance of ARGs in soil (P < 0.01), and also markedly shifted the bacterial composition that was significantly correlated with ARGs profiles. Manure-borne microorganisms contributed largely to the elevation of ARGs due to both the addition of manure-borne antibiotic resistant bacteria (ARB) in soil and potential horizontal gene transfer (HGT) via mobile genetic elements (MGEs) from manure-borne ARB to indigenous soil microorganisms. In contrast, indigenous soil microorganisms were demonstrated to prevent the dissemination of ARGs from manure to soil. The reason could be due to that indigenous soil microorganisms prevented the invasion and establishment of manure-borne ARB in soil. The abundance of ARG in manured soil decreased over time, but was still higher than that in control soil, indicating the persistence of ARGs in manured soil. These findings may shed light on the mechanisms underlying the spread and fate of ARGs in manured soil and also clues for ARGs mitigation.