Excessive use of chemical fertilizers deteriorates the soil environment and limits the normal growth of Arabica coffee trees. In order to identify the optimal coupling mode of chemical fertilizer application and biomass return that enhances the soil ecological environment and promotes the photosynthetic efficiency of Arabica coffee, this study investigated the impacts of three levels of inorganic fertilizers (FL: 360 kg·ha−1, FM: 720 kg·ha−1, and FH: 1080 kg·ha−1) and three types of coffee husk returning methods (CB: coffee husk biochar, CC: coffee husk compost, CA: coffee husk ash) on the soil fertility, microbial amount, enzyme activity, and photosynthetic characteristics of the Arabica coffee root zone. The entropy weight-TOPSIS method was employed to evaluate the comprehensive benefits. The results showed that FM had the biggest effect on improving soil fertility, microorganisms, and enzyme activities compared with FL and FH. Moreover, compared to CA, CC significantly increased soil organic carbon, organic matter, and total nitrogen content. CC significantly enhanced the activities of soil phosphatase and urease, respectively, by 29.84% and 96.00%, and significantly increased the amount of bacteria, fungi, and actinomycetes by 62.15%, 68.42%, and 46.21%, respectively. The net photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs) of FMCC were significantly higher than those of other treatments. The comprehensive benefit evaluation of the soil environment and photosynthetic characteristics by the entropy weight-TOPSIS method ranked FMCC first. Therefore, FMCC was the optimal coupling mode for fertilizer application and the coffee husk returning method. The findings of this study not only provide scientific guidance for fertilizing Arabica coffee but also clarify the proper approach to returning coffee husk to the field, thereby improving soil ecology and promoting green and efficient production of specialty crops.