Given that farmland serves as a strategic resource to ensure national food security, blind emphasis on the improvement of food production capacity can lead to soil overutilization and impair other soil functions. Hence, the evaluation of soil health (SH) should comprehensively take soil productivity and ecological environmental effects into account. In this study, five functions from the perspective of functional soil management were summarized, including primary productivity, provision and cycling of nutrients, the provision of functional and intrinsic biodiversity, water purification and regulation, and carbon sequestration and regulation. For each soil function, in view of the natural and ameliorable conditions affecting SH, basic indicators were selected from the two aspects of inherent and dynamic properties, and restrictive indicators were chosen considering the external properties or environmental elements, with the minimum limiting factor method coupled with weighted linear model. The new evaluation system was tested and verified in Yixing City, China. The healthy and optimally functional soils were concentrated in the northeast and mid-west of Yixing City, whereas unhealthy soils were predominant in the south and around Taihu Lake. The main limitations to SH improvement included cation exchange capacity, nutrient elements, and soluble carbon. The SH evaluation method was verified using the crop performance validation method, and a positive correlation was noted between food production stability index and soil health index, indicating that the evaluation system is reasonable.