In light of growing concerns regarding food security and soil health, there is increasing emphasis on the assessment of soil health and efforts to improve or maintain the soil health of cultivated land. This case study Niutian Town in Jiangxi Province in southern China was selected as a typical red soil and a major grain-producing area. This research involves an integrated evaluation model based on Entropy weight TOPSIS and emergy analysis to assess the soil health of cultivated land. An evaluation system was developed, comprising 31 indicators selected on the basis of resources and environments, with an emphasis on sensitive and promising microorganisms category indicators. Additionally, experiments were conducted to assess the ecological risk of soil pollution and develop novel soil conditioners. Our results indicate that Pb, Hg and Cd present a moderate ecological risk on 92.1% of the cultivated land. Furthermore, 56.8% of the cultivated land was ‘sub-healthy’ or ‘unhealthy’. Biochar was found to be a soil conditioner with a good adsorption effect, with absorption rates reaching up to 99.9% and 88.3% for Pb and Cd, respectively. Additionally, g-C3N4 was added to address pesticide contamination, which showed an adsorption rate of up to 75.2% for atrazine. This work develops a targeted remediation approach based on assessment results to address regional cropland soil health issues.