The quality of soil is essential for ensuring the safety and quality of agricultural products. However, soils contaminated with toxic metals pose a significant threat to agricultural production and human health. Therefore, remediation of contaminated soils is an urgent task, and humic acid (HA) with hydroxyapatite (HAP) materials was applied for this study in contaminated alkaline soils to remediate Cd, Pb, Cu, and Zn. Physiochemical properties, improved BCR sequential extraction, microbial community composition in soils with superoxide dismutase (SOD), peroxidase (POD), and chlorophyll content in plants were determined. Among the studied treatments, application of HAP-HA (2:1) (T7) had the most significant impact on reducing the active forms of toxic metals from soil such as Cd, Pb, Cu, and Zn decreased by 18.59%, 9.12%, 11.83%, and 3.33%, respectively, but HAP and HA had a minor impact on metal accumulation in Juncao. HAP (T2) had a beneficial impact on reducing the TCleaf/root of Cd, Cu, and Zn, whereas HAP-HA (T5) showed the best performance for reducing Cd and Cu in EFleaf/soil. HAP-HA (T5 and T7) showed higher biomass (57.3%) and chlorophyll (17.9%), whereas HAP (T4) showed better performance in POD (25.8%) than T0 in Juncao. The bacterial diversity in soil was increased after applying amendments of various treatments and enhancing metal remediation. The combined application of HAP and HA effectively reduced active toxic metals in alkaline soil. HAP-HA mixtures notably improved soil health, plant growth, and microbial diversity, advocating for their use in remediating contaminated soils.