Soil fungi constitute multiple functional communities essential for organic matter decomposition. Cover crops stabilize sustainable crop production by introducing exogenous organic matter to mitigate chemical fertilizationinduced soil degradation. But responses of wheat growth to soil characteristics and fungal functionality communities under combined impacts of cover crop and nitrogen fertilization were not obviously elucidated. Herein, the long-term interactive experiments of cover crop and nitrogen fertilization revealed that cover crop increased soil organic carbon by an average of 18% and increased soil mineral-associated organic carbon by 13%, while fertilization increased them by an average of 8% and 7%, respectively. Legume cover crop reduced soil bulk density by 7%-8%, but increased soil water content by 8%-31% among distinct fertilizations. Soil fungal functional communities were mainly composed of the saprotroph communities, their diversity generally had the highest values in the middle fertilization in each cover crop. Meanwhile, cover crop and fertilization singly and interactively had stronger effects on the pathotroph and symbiotroph community compositions, respectively. Stochastic processes governed the saprotroph and pathotroph communities, while deterministic processes intensified along with elevated fertilization. Networks of soil fungal functionality communities were composed of specialized modules consistently containing diversified trophic mode phylotypes. Overall, wheat growth indicated by wheat biomass and grain yield was enhanced by optimal fertilization rate in legume cover crop. Moreover, wheat growth was primarily regulated by the direct effects of pathotroph community composition and the total effects of fertilization and soil characteristics based on partial least squares path modeling. These findings suggest that optimal combinations of cover crop and nitrogen fertilization can benefit crop production through regulating soil characteristics and fungal functionality communities, which likely serves as a valuable reference for cover crop agricultural system to balance the management of cover crop and nitrogen fertilization.