Decomposition is an important process in the nutrient cycling of agricultural ecosystems, and it is also crucial in affecting soil fertility and productivity o f farmland. Land use not only significantly affects the structure of micro-decomposer, including soil microorganisms and nematodes in farmland, but may also change their ecological functions, which affects decomposition consequently. However, it is still unclear how habitat changes in agroecosystems affect the decomposition rate, nor are the dynamic relationships between environmental factors, soil biota, and decomposition under different land use types. In this study, the 'tea bag index' was used to quantify the decomposition rate of farmland, fallow land, economic woodland and mixed woodland in the typical agricultural areas of Pengzhou City. The differences in environmental factors as well as the community structure and functions of soil micro-decomposers between habitat types were compared. The results showed that the decomposition rate was the highest in mixed woodland and fallow land, followed by economic woodland and farmland. The abundance of soil micro-decomposers was relatively higher, and the food web tended to be more mature and stabilized in the woodland. In farmland and economic woodland where agricultural management is more frequent, the abundances of symbiotic and saprophytic fungi were significantly lower, and the connectivity of decomposer food web was weaker, but the abundance of pathogenic bacteria was also lower than those in less disturbed semi-natural habitats. Soil bacteria was the most important biotic factors to regulate the decomposition rate. The increased aboveground plant richness, soil pH, bulk density and carbon content contributed to accelerating decomposition. The implementation of agroforestry and intercropping in Pengzhou, improvement of habitat complexity and rational human management can better maintain the complexity and connectivity of decomposer food webs, which can promote rapid and thorough decomposition. This is of great significance in maintaining soil nutrients and health, and promoting productivity.