Soil fauna is an important part in the soil ecosystem and plays important roles in material cycling. Furthermore, soil fauna, which is affected by tillage of the soil, is a good indicator species for the soil environment. The Song-nen plain is an important area for food production in China. To investigate the spatio-temporal distribution characteristics of meso-micro soil fauna in cultivated blacksoil in the Song-nen plain area, five typical areas, including Hulan, Suihua, Hailun, Yian, and Nenjiang, were chosen from southeast to northwest in the Song-nen plain. The study was conducted in May, August, and October 2009. Our study will provide a fundamental theory and method for biodiversity conservation and land management in the cultivated blacksoil area. Samples of meso-micro soil fauna were collected from soil layers at depths of 0-5, 5-10, 10-15, 15-20 cm. We extracted and identified 15,058 individuals, belonging to 54 groups. Among them, Oribatida, Prostigmata, and Isotomidae were the dominant taxa, amounting for 69.94% of the total individuals in the soil fauna. The eight common groups were Mesostigmata, Hypogastridae, Entomobryidae, Chironomidae, Onychiuridae, Sminthuridae, Nematoda, and Staphylinidae larvae, totaling 25.20% of all individuals. The results derived from this research are as follows: (1) Differences in soil faunal characteristics were observed in different sampling areas (P < 0.01). The density of meso-micro soil fauna was highest in Hailun, whereas it was lowest in Nenjiang. The group number and richness index of meso-micro soil fauna were highest in Suihua, and were lowest in Nenjiang. The Shannon-Weiner and Evenness indices for meso-micro soil fauna were highest in Hailun, and lowest in Yian. The Simpson Dominance index was highest in Hailun, and lowest in Hulan. (2) Seasonal variation exerted a significant influence on community structure of soil fauna in the cultivated blacksoil area. The number and density of meso-micro soil fauna were significantly higher in October than in other months (P < 0.01). The Evenness and Richness indices of meso-micro soil fauna were significantly higher in August than in other months (P < 0.05). The Simpson Dominance index was significantly lower in August than in other months (P < 0.05). (3) Number of individuals and groups of soil fauna gradually decreased with depth. In addition, in different areas there were differences in the stability of the vertical distribution of soil fauna among seasons. There were not distinct differences in the number of individuals of meso-micro soil fauna in different soil layers in May, but there were significant differences in August and October. The number of individuals was much greater in the 0-5 cm layer than in other layers, and an obvious aggregation on the surface occurred in August and October. (4) Concerning the relationship of soil fauna and the soil environment, the values of pH, total nitrogen, and total phosphorus in cultivated black soil were strongly correlated with the community structure of soil fauna (P < 0.05). The number of individuals, Evenness index, Richness index, and density of soil fauna were closely related to soil physicochemical properties (P < 0.05), whereas the numbers of dominant and common groups were closely associated with total phosphorus, the carbon-nitrogen ratio, and total organic carbon in the soil.