Using long-term field experiment of different ecosystems established at the Hailun State Key Experimental Station of Agroecology, Chinese Academy of Sciences, soil profiles down to the parent material layer (200 cm) were collected to investigate microbial metabolic characteristics of the carbon source by using the Biolog ECO micro-plate technique. The field treatments included three different ecosystems:Crop Land (CL), Grass Land (GL), and Forest Land (FL). The results showed that soil organic carbon (SOC), total nitrogen (TN), and effective nitrogen (EN) decreased with soil depth; soil pH increased with soil depth, and it was lower in the surface layer (0-20 cm) than in the bottom layer (180-200 cm). The number of cultivable microorganisms (bacteria, fungi, and actinomycetes) gradually decreased with soil depth; the cultivable microorganisms mainly lived in the top 0-60 cm soil layer. The numbers of the three types of cultivable microorganisms decreased in the order of GL > CL > FL at 0-20 cm soil depth, and the numbers were almost the same in the three ecosystems in the 60-200 cm soil layer. Activities of the soil microbial community were the highest at 0-40 cm soil depth and decreased with soil depth; the lowest value was observed in the 200 cm soil layer. Similar to SOC and TN, the Shannon diversity index and carbon source utilization gradually decreased with soil depth and showed a positive correlation with SOC and TN (P < 0.05). Compared to CL, carbon use efficiency of the soil microbial community improved at subsurface soil depth (20-40 cm) in GL and FL. This demonstrated that the roots of the vegetation could break the plow pan in GL and FL soils without any tillage activities and promote the activities of the soil microbial community below the surface soil layers. Principal component analysis of the utilization intensity of six types of carbon sources showed that the different long-term ecosystems with different vegetation types had changed the carbon utilization intensity of the soil microbial community in the soil profiles. The roots of the vegetation or crops had great influence on the soil microbial community to 100 cm depth, but not to 200 cm depth.