Flue gas desulphurization gypsum (FGD) is a major solid waste in coal-fired energy plants, and the appropriate reuse of this resources is still a major challenge. In this study, the feasibility of FGD as a calcium source to produce hydroxyapatite (FGD-HAP) for the immobilization of lead (Pb) and cadmium (Cd) in spiked soil was investigated. The effects of FGD and FGD-HAP on soil properties and redistribution, bioaccessibility and plant uptake of Pb and Cd were examined. Results showed that application of FGD and FGD-HAP could significantly improve the enzymes activities of contaminated soils, but the effectiveness was more pronounced with FGD-HAP. Addition of only 1% FGD-HAP could effectively reduce bioavailable Pb and Cd concentration in soil as measured by CaCl2 extraction by 60.6% and 65.4%, respectively. On the other hand, plant available Pb and Cd could significantly decrease by 93.8% and 73.2% after amendment of 5% FGD-HAP. Significant changes in the micro-scale distribution of heavy metals before and after FGD-HAP treatment demonstrated that while heavy metals were predominantly associated with iron/manganese oxides in untreated soil, high correlation between heavy metals and phosphorus/sulfur was observed in FGD-HAP treated soil. In addition, results of the leaching tests showed that incorporation of FGD-HAP enhanced the retention capacity of heavy metals in soil, indicating that application of FGD-HAP could diminish the environmental risk of leachable heavy metals to groundwater. Overall, this study highlighted the potential value of FGD-HAP as a low-cost and high-efficient amendment for remediation of Pb and Cd contaminated soils.