Different understory herbaceous management practices affect orchard soil health, and understanding the mechanisms by which sod cultivation and herbicide weed control affect soil nutrient cycling can help optimize the management in orchards. In this study, the differences in soil nutrient content, enzyme activities and abundance of functional microbial genes were compared after 5 years of sod cultivation and herbicide weed control treatments in a citrus orchard. The results showed that compared to herbicide weed control, sod cultivation significantly increased soil N, P content, and soil urease, sucrase, and phosphatase activities. Sod cultivation increased soil microbial α diversity, and increased the abundance of functional genes for denitrification and 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 nutrients content, enzyme activities, and functional gene abundance. This study demonstrated that sod cultivation promotes 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 nitrogen and phosphorus transformation. Compared with the use of herbicides to control weeds, it is more conducive to maintaining the soil health of citrus orchards.