The combined application of organic materials and chemical fertilizers is an effective approach for improving crop productivity and soil quality. Purple soil is characterized by low N, P, and organic C contents that influence crop productivity. However, the optimal organic materials that can be used to improve purple soil quality and crop yields remain to be clarified. Here, we conducted a 13-year field experiment (from 2007 to 2019) in Sichuan Province, China, intending to assess the long-term influence of various combinations of organic materials and chemical fertilizers on soil enzymatic activities, microbial communities, and crop yields. Treatments included chemical fertilizer alone (NPK), NPK plus returned straw (NPKS), NPK plus pig manure (NPKM), NPK plus fungal residue (NPKF), and NPK plus green manure (Vicia villosa Rothvar.) (NPKG). Results showed that NPKM and NPKF treatments significantly increased the average yields of maize (7.9 and 6.4%, respectively) and wheat (15.7 and 12.9%, respectively) relative to NPK treatment. The highest sustainable yield index value of maize and wheat was observed in NPKF treatment. The long-term application of fungal residue (NPKF) significantly increased soil organic C and available P contents, relative to NPK、NPKS and NPKG treatments, and soil organic C content increased from 6.95 to 9.12 ± 1.06 g kg⁻¹ and available P content from 6.87 to 12.26 ± 2.23 mg kg⁻¹. Relative to NPK treatment, NPKF treatment significantly enhanced soil microbial biomasses (C, N, and P) and soil C-, N- and P-cycling enzyme activities but significantly decreased soil pH. The soil enzyme index following NPKF treatment was significantly higher relative to other treatments and was 208.6% higher than NPK treatment. Additionally, relative to NPK treatment, NPKF treatment altered soil microbial community structure, and significantly increased the rate of G⁺/G⁻ and cy19/18:1ω7c. Soil microbial biomasses N, Nitrate N, and available P were the main factors regulating the change of microbial community in purple soil. We, therefore, conclude that NPKF treatment is an effective fertilization strategy for improving purple soil quality and crop yields.