Retaining carbon in cultivated soils is an important mechanism to mitigate climate change and to maintain the sustainability of agricultural ecosystems. Characterization of the soil microbial community was an early means to quantify the increase in soil organic carbon (SOC) content and stability under different cropping systems. However, the effects of different cropping systems on the soil microbial community and enzyme activity and the driving force for increasing the SOC content remain unclear, especially the differences between continuous maize (Zea mays L.) cropping and rotation systems containing legumes. We used a long-term field experiment (30 years) in the Mollisol region of Northeast China. The field experiment was undertaken in split-plot design comprised of four treatments: i) farmland fallow (FALL), ii) continuous soybean cropping (CSC), iii) maize-soybean rotation (MSR), iv) continuous maize cropping (CMC). Fluorometric assays and phospholipid fatty acid analysis (PLFA) were used to determine the biological characteristics of the soil. The SOC chemical composition was characterized using Cross Polarization/Magic Angle Spinning solid-state 13C-nuclear magnetic resonance (13C NMR) spectroscopy. Principal component analysis (PCA), redundancy analysis (RDA) and the partial least squares path model (PLS-PM) were used to explore the coupling mediation of these parameters further. Our results suggested that soil microbes in the four systems were not limited by C and N, but co-limited by P. But compared with the FALL system, the CMC system significantly alleviated the phosphorus limitation of the microorganisms. The CMC system also significantly increased soil nutrient content, especially SOC content (40.8%), available phosphorus (117%), available potassium (30.3%), NO3−-N (148%), and increased microbial community abundance and enzyme activities. Compared with the CMC system, the MSR system held relatively lower Gram-positive: Gram-negative ratio and higher fungi: bacteria ratio, which indicated that the soil microbial community structure is more conducive to improving the SOC stability. Meanwhile, more evidence supporting data that SOC stability was enhanced in MSR soils was provided by the 13C NMR spectra and higher-quality indices (A / AO, AI, HI and LCI). Moreover, strong correlations and RDA analysis confirmed that SOC is the main factor affecting microbial communities and enzyme activities.