Inversion tillage and organic fertilizer application can break the plow pan and improve soil quality. However, the effects of combining these practices on the soil microbial resource limitation and maize yield in Haplic Chernozem are unclear. In this research, a field experiment was established in 2018, and soil samples were collected in 2021 in Longjiang County in Northeast China, which is a Haplic Chernozem region. Four treatments comprising conventional tillage (T15), conventional tillage with organic fertilizer (T15+M), inversion tillage (T35), and inversion tillage with organic fertilizer (T35+M) were randomly arranged with four replications. Compared with T15 and T15+M treatments, soil bulk density significantly decreased by 11.1–16.3% in the 15–35 cm layer under T35 and T35+M treatments, accompanied by the improvement in soil pore structure (e.g., soil porosity, circularity, and Euler number). T15+M treatment significantly increased soil organic carbon and soil nutrient contents by 11.1–16.3% and 3.9–24.5% in the 0–15 cm layer compared with other treatments. However, soil organic carbon, total nitrogen, available phosphorus content, microbial biomass, and enzymatic activities reached the maximum values in the 0–35 cm layer under T35+M treatment. In addition, T35+M treatment had the highest maize yield and sustainable yield index. Extracellular enzymatic stoichiometry suggested that soil microorganisms are generally co-limited by carbon and phosphorus in Haplic Chernozem. However, T35+M treatment significantly reduced soil microbial resource limitation, which was one important factor impacting maize yield and sustainability. Random-forest and partial least-squares path modeling showed that T35+M treatment could reduce soil microbial resource limitation and increase the stability and sustainability of the maize yield by improving soil available nutrients, microbial biomass, and pore structure. Therefore, the incorporation of inversion tillage and organic fertilizer is a suitable soil management practice in view of increasing soil quality and crop yields in a Haplic Chernozem region.