Long-term (10 years) application of conservation tillage following conversion from conventional tillage (CT) can achieve a new equilibrium in the soil environment, which is vital to reverse soil biodiversity declines and fulfil the goal of maintaining agroecosystem sustainability. However, in such a situation, how the soil community regulates nutrient cycling impacting crop yield is not well documented. Therefore, the relations between mineralized nitrogen (N) delivered by soil food web and soybean (Glycine max Men.) yield were investigated after 14 years application of CT, reduced tillage (RT) and no tillage (NT) in a black soil (Typic Hapludoll) of Northeast China. We hypothesized that soil mineralizable N would increase with the complexity of the soil food web, and that the trophic groups involved in associating N mineralization with crop yield will vary with soil depth in the conservation tillage practice. During the soybean growing season, soil organisms, including bacteria, fungi, nematodes, mites and collembolans, were extracted and identified monthly from 0-5 and 5-15 cm soil depths to estimate the complexity of the food web indicated by the species richness and connectance indices, and to simulate the mineralized N using energetic food web modelling. The species richness and connectance of the food web at both soil depths were significantly affected by tillage practices, and their values decreased of the order of NT > RT > CT. A similar trend was also revealed for the simulated N mineralization, that is, the mineralized N released either from the functional feeding guilds or from the energy pathways of the food web were greater in RT and NT than in CT at both soil depths. Multiple linear regression analysis showed that soil organisms involved in coupling the mineralized N with soybean yield were different at different soil depths, in which fungal and root pathways at 0-5 cm and bacterial pathway at 5-15 cm were the driving factors for the supply of mineralized N to soybean in NT and RT soils. These results support our hypothesis and highlight the essential role of soil food web complexity in coupling N mineralization and crop yield after long-term application of conservation tillage. Additionally, the current modelling work provides basic hypotheses for future studies to test the impact of soil biodiversity or specific functional guilds on the fate of N in agro-ecosystems.