Cover crops are an increasingly important component of sustainable agriculture, as they can improve soil quality and productivity. However, how cover crops affect soil health and multi-nutrient cycling is not well understood. To address these issues, here, we established a long-term (15-year) field experiment to evaluate the influence of several cover crop treatments (legumes vs. non-legumes vs. mixture crop (legumes + non-legumes)) in a Carya cathayensis plantation on soils. We found that cover crops greatly increased both the soil health index and multi- nutrient cycling in both surface soil (0-20 cm) and subsurface soil (20-40 cm), especially in the mixed cover crop treatment, by enhancing several soil biochemical properties. In addition, cover crops lead to higher carbon (C), nitrogen (N), and phosphorus (P) acquisition enzyme activities. Enzyme stoichiometry analyses showed that microbial activity in the surface soil was mainly P-limited, whereas C-limitation was more pronounced in the subsurface soil. The reduction of C limitation in the cover crops subsurface soil contributes to microbial C turnover, potentially increasing soil C sequestration. Importantly, we found that soil health index was positively correlated with multi-nutrient cycling regardless of soil depth. However, increased microbial metabolic limitation in the subsurface soil detrimental to the maintenance of soil health and multi-nutrient cycling. Furthermore, soil nutrients regulate soil health index and multi-nutrient cycling by influencing microbial resource limitation. Overall, our study illustrates that the use of cover crops, especially cover crop mixtures in the long term can foster soil health and contribute to improved soil multi-nutrient cycling, and can be used as an effective sustainable agricultural management practices.