The lime concrete black soil (LCBS) is a typical soil with low productivity and fertility in China. Increasing soil organic matter is extremely important for the improvement of LCBS, but little is known about the relationship between soil organic matter and microbial community characteristics in the LCBS. Here, we collected 40 LCBS samples in the North Jiangsu Plain, measured soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon (DOC), microbial biomass carbon (MBC) and microbial carbon use efficiency (CUE), and employed high-throughput sequencing technology to determine the bacterial community structure. The results showed that SOC content in LCBS was 15.82 g/kg, but DOC accounted for a very small fraction of SOC (approximately 2‰), indicating that C availability is low in LCBS. Xanthomonadaceae, Gaiellaceae, and Acidobacteriaceae families dominated soil bacterial community. However, there were low abundance of the bacteria associated with C sequestration such as acidobacteria and actinomycetes. The low CUE (ranged from 0.07 to 0.20) was significantly correlated with SOC and DOC. The results suggested that soil organic matter formation and accumulation are restricted in part by the low carbon use efficiency and poor structure of microbial community in LCBS.