Intensive long-term production has increasingly aggravated soil health degradation in citrus orchards of Zhejiang Province. Conventional evaluation systems, however, remain heavily biased towards routine chemical properties and inadequately account for organic carbon fractions and biological indicators, thereby failing to capture the full picture of soil functional deterioration. In this study, soil samples were collected from major citrus-producing areas of Zhejiang, and a comprehensive set of physicochemical properties, carbon fractions, enzyme activities and microbial diversity indices was systematically measured. A minimum data set (MDS) was constructed via principal component analysis combined with correlation analysis, on which a soil health evaluation model was built and used to diagnose key obstacle factors. The results showed that the MDS for soil health evaluation of Zhejiang citrus orchards in comprised seven indicators, i.e., dissolved organic carbon, alkali-hydrolyzable nitrogen, acid phosphatase, β-glucosidase, Chao1 index, particulate organic carbon and mineral-associated organic carbon. Obstacle factor diagnosis identified soil organic carbon, mineral-associated organic carbon, available phosphorus, microbial biomass carbon and Chao1 index as the primary limiting factors. The above analyses collectively demonstrate that carbon fractions and microbial diversity indicators play a key driving role in citrus orchard soil health. Moreover, after excluding these indicators, the stability of the evaluation system and its predictive capacity for citrus yield and quality decreased significantly, further confirming that these two categories of indicators are indispensable in soil health evaluation of citrus orchards. The MDS?based framework developed in this study reduces the number of indicators by approximately 66% while maintaining scientific robustness, thus offering both practicality and scalability. It provides a theoretical basis for precision diagnosis and targeted management of soil health in Zhejiang’s citrus orchards, and may also serve as a methodological reference for soil evaluation in other orchard systems.