The impacts of prolonged nutrient-deficiency fertilization on the rhizosphere soil microbial community and crop yield remains largely underexplored. This study analyzed rhizosphere soil samples collected from a 30-year cassava monoculture field, comprising six fertilization treatments: balanced fertilization (NPK), nitrogen deficiency (PK), phosphorous deficiency (NK), potassium deficiency (NP), no fertilization (-NPK) and 50% NPK supplemented with burned soil (FNPK). Measurements included storage root yield, soil properties, and microbial community. Compared to NPK treatment, deficiency fertilization (PK, NK, NP, and -NPK) significantly decreased cassava yield by 38.6%, 21.3%, 38.1%, and 61.6%, respectively, while FNPK treatment maintained yield levels. The NK treatment intensified soil acidification, and the NP treatment accelerated soil organic carbon depletion. Conversely, FNPK treatment significantly improved rhizosphere soil pH and nutrients content. Long-term deficiency fertilization showed no significantly impact on bacterial and fungal richness (Chao1 index) and diversity (Shannon index), whereas FNPK markedly increased bacterial richness and diversity and modified bacterial and fungal β-diversity in rhizosphere soil. Soil pH was emerged as the primary driver of microbial community shifts. Bacterial communities in FNPK treatment exhibited reduced abundance in Acidobacteriota and Crenarchaota phyla and an increase in genus RB41 of Acidobacteriota and MND1 of Proteobacteria. FNPK also shifted the dominant fungal phyla from Ascomycota to Basidiomycota, and reduced the genus Melanconiella, associated with decreased plant wilt incidence. Treatments PK, NK, and -NPK suppressed the functional abundance of key bacterial and fungal groups, whereas FNPK significantly enhanced bacterial Chemoheterotrophy function, positively correlated with yield, and increased the abundance of undefined saprotrophic and arbuscular mycorrhizal fungal functional groups. Collectively, these findings indicate that prolonged nitrogen-based chemical fertilization intensifies soil acidification, adversely affecting the composition and function of soil microbial communities. The integration of burned soil with chemical fertilizer demonstrates potential in enhancing soil fertility and microbial diversity, offering insights for optimizing fertilization strategies in tropical cassava production systems.