In this study, the differences in soil nutrient contents, enzyme activities and abundance of functional microbial genes were compared after 5 years of sod cultivation (SC) and herbicide weed control (HWC) treatments in a citrus orchard. The results showed that compared to HWC, SC significantly increased the contents of soil nitrogen (N) and phosphorus (P), the activities of soil urease, sucrase and phosphatase. Meanwhile, SC increased soil microbial α diversity, and increased the abundance of functional genes for denitrification, organic degradation and synthesis in the nitrogen cycle, and the abundance of functional genes for oxidative phosphorylation and transporters in the phosphorus cycle. Positive correlations were observed among soil nutrient contents, enzyme activities, and functional gene abundance. This study demonstrated that SC can promote soil nutrient cycling and increase the availability of soil nutrients by enhancing the abundance of key functional genes and the activities of enzymes during the processes of soil N and P transformation, thus, it is more conducive to maintaining soil health of citrus orchards compared with HWC.