Soil microbes are the most vital decomposers in terrestrial ecosystems, and play a crucial role in wetland carbon (C), nitrogen (N), and phosphorus (P) cycles. Several studies have been conducted on the microbial biomass in the forests, plateaus, grasslands, and farmland; however, few studies on soil microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial biomass phosphorus (MBP) have been conducted in the chenier of the Yellow River Delta, especially studies of the spatial distribution of soil microbial biomass C, N, and P in different habitats. To investigate the soil fertility of different habitats, the soil microbial biomass C, N, P and physicochemical properties were observed in five soil layers (0-5, 5-10, 10-20, 20-40, 40-60 cm) of the high tide line, seaward side, dune crest, and landside of the chenier of the Yellow River Delta. The results showed that the microbial biomass C, N, and P of different habitats were ranked as follows:dune crest > landside > high tide line > seaward side. The microbial biomass C, N, and P displayed an obvious vertical distribution in decreasing order of 0-5 cm > 5-10 cm > 10-20 cm > 20-40 cm > 40-60 cm. Soil microbial biomass C, N, and P accounted for 1.09%-3.48%, 2.62%-7.27%, and 0.78%-2.86% of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP), respectively. There were no significant differences between the ratio of microbial biomass carbon to soil organic carbon (MBC/SOC) in the dune crest, landside, and high tide line (P > 0.05), but they were significantly higher than those on the seaward side (P < 0.05). The changing trend of the ratio of microbial biomass nitrogen to total nitrogen (MBN/TN) and the ratio of microbial biomass phosphorus to total phosphorus (MBP/TP) were the dune crest and landside > seaward side and high tide line. The abiotic limiting factors of soil microbial biomass C, N, and P were soil water content, pH value, and salt content in the dune crest and landside. The abiotic limiting factors of soil microbial biomass C, N, and P were water content and pH value in the seaward side and high tide line areas. The positive correlations between soil microbial biomass C, N, and P and soil nutrients were significant or extremely significant in the dune crest, landside, and high tide line. The coordination and stability were higher, indicating that soil microbial biomass C, N, and P could be used as biological indices to evaluate soil fertility in the chenier of the Yellow River Delta, which provides a theoretical basis for soil fertility management and vegetation restoration of cheniers in the Yellow River delta.