A 7-year multisite field experiment was performed to assess the relative importance of climate, soil, and microbial properties in crop production in a wheat cropping system under contrasting fertilization management (i.e., continuous organic vs. chemical fertilization). The results showed that continuous organic application significantly increased the annual grain yield by 11.0%-15.4% compared to chemical fertilization. Soil organic carbon was significantly enhanced by 38.0% following organic fertilization, which was partially explained by the increased abundances of functional genes involved in carbon fixation, such as acsB and rbcL. Continuous organic application increased the soil pH at each experimental site, which led to a significant enhancement in bacterial richness (i.e., Chao1) and diversity (i.e., Shannon index). Notably, organic application favored the growth of Proteobacteria and Actinobacteria but reduced the abundances of Bacteroides, Verrucomicrobia, and Acidobacteria, which ultimately led to a more complicated bacterial co-occurrence network. The results of the structural equation model (i.e., SEM) indicated that the annual air temperature and soil pH exerted the largest positive and negative direct effects on crop productivity, respectively, under continuous chemical fertilizer application, However, the bacterial community structure (i.e., nonmetric multidimensional scaling, NMDS) and Shannon diversity index were the most important factors in crop production when organic fertilizer was applied continuously. Variance partitioning analysis further found that climate, soil, bacterial community, and potential function explained 35.9%, 31.6%, 19.2% and 13.4% of the overall variance in crop productivity, respectively, under chemical fertilization, and these values were 34.3%, 11.4%, 32.9% and 21.3%, respectively, when organic fertilizer was applied. These findings suggest that continuous organic application reduces the contribution of climate and edaphic conditions to crop yield compared to chemical fertilization but strengthens the associations between soil microbial function and crop production. Overall, this work provides new insights into the complexity of fertilization-induced climate-plant-microbial interactions and highlights the importance of intensified biological interactions on the sustainability of cropping ecosystems
