The degradation of black soil is a serious problem with the decrease in soil organic matter (SOM) content in northeast China, and animal manure as a reservoir of antibiotic resistance genes (ARGs) is commonly amended into soil to sustain or increase the SOM content. However, the potential effect of SOM content on soil resistome remains unclear. Here, a soil microcosm experiment was established to explore the temporal succession of antibiotic resistance genes (ARGs) and bacterial communities in three black soils with distinct difference in SOM contents following application of poultry manure using high-throughput qPCR (HT-qPCR) and MiSeq sequencing. A total of 151 ARGs and 8 mobile genetic elements (MGEs) were detected across all samples. Relative abundance of ARGs negatively correlated with SOM content. Manure-derived ARGs had much higher diversity and absolute abundance in the low SOM soils. The ARG composition and bacterial community structure were significantly different in three soils. A random forest model showed that SOM content was a better predictor of ARG pattern than bacterial diversity and abundance. Structural equation modeling indicated that the negative effects of SOM content on ARG patterns was accomplished by the shift of bacterial communities such as the bacterial diversity and abundance. Our study demonstrated that SOM content could play an important role in the dissemination of ARGs originated from animal manures, these findings provide a possible strategy for the suppression of the spread of ARGs in black soils by increasing SOM content.