Abstract: Soil health has become a limiting factor in the development of modern protected agriculture. Understanding the importance and underlying regulatory mechanisms of soil health and designing approaches towards healthy soil management are important guidelines for improving soil productivity and sustainable development in facility agriculture. In this article, the connotations of soil health in protected agriculture and its evaluation indicators are summarized. Furthermore, this paper reports existing problems, such as a high replanting index, continuous crop obstacle, and soil-borne diseases that may restrict healthy soil management. Next, we discuss techniques that are based on crop and soil regulation to improve soil health, including optimizing planting structures, cultivating resistant varieties, regulating nutrients, building artificial microbial communities, and regulating soil food webs. Finally, this article suggests that a soil health evaluation system for facility agriculture should be constructed, and new regulatory techniques should be introduced to provide a reference for more in-depth research on soil health improvement for protected agriculture.