Soil fertility plays a key role in citrus productivity. Therefore, it is necessary to explore the effects of soil amendments on soil fertility and citrus productivity and estimate carbon fractions’ suitability, which response to soil fertility and citrus productivity. A field experiment in a citrus orchard was conducted containing five treatments: local habit fertilization (LF), special fertilizer [25% lower NPK than LF, (SF)], special fertilizer, and rice straw mulching [0%, 12.5%, and 25% NPK higher than LF (SFRS25, SFRS37.5, and SFRS50, respectively)]. Total organic carbon (TOC), microbial biomass carbon (MBC), water-soluble organic carbon (WSOC), permanganate oxidizable carbon (ROC), available N, P, K, fruit yield, and quality were analyzed. Straw mulching and special fertilizer significantly increased soil carbon fractions, such as MBC and ROC. Such treatments also enhanced the soil available N, P, and K, subsequently elevated the fruit yield. MBC, available K, and available P showed a significantly positive correlation with citrus yield. Redundancy analysis indicated that MBC and ROC significantly explained 61.87% of the variation for available nutrients, suggesting that the increase of organic carbon fractions and microbial biomass could accelerate nutrient cycling for the plant. It proved that decrement application of special compound fertilizer with straw mulching raised fruit yield by altering soil carbon fractions to improve soil available nutrients or fertility. The MBC of soil labile carbon responded more sensitively to not only soil fertility but also citrus fruit yield.