【Objective】Paddy soils are extensively polluted by heavy metals (HMs) in China and present significant challenges for safe agricultural use. Thus, this study seeks to address the heavy metal pollution in China's paddy soils, focusing on polluted soils from the Dabaoshan mining areas in Shaoguan, Guangdong Province.【Method】A flooding-drainage incubation experiment was conducted and combined with chemical extraction, diffusive gradients in thin films (DGT) technology, and correlation analyses. Also, the impact of phosphorus (P) and humic acid (HA) addition on soil Fe speciation and the bioavailability of related elements was evaluated. The selection of P and HA concentrations was based on common agricultural practices to ensure the environmental relevance of our findings.【Results】The results revealed that soil pH gradually became neutralized while Eh decreased during the flooding period. The concentrations of acid-soluble Fe2+, amorphous Fe, and Fe activation degrees increased from 1.5 g·kg-1 to 4.8 g·kg-1, 6.6 g·kg-1 to 10.1 g·kg-1, and 21% to 29%, respectively, with a decrease in amorphous Fe content observed in treatments with added P and HA from 2 to 42 days of flooding. After soil drainage, both Feox and Fe activation degree rapidly decreased to 7.4 g·kg-1 and 21.6%. Regarding CaCl2-extractable heavy metals, the lowest values were observed after 14 days of flooding, whereas levels of As, Cd, Cu, and Zn rapidly increased to 0.1 mg·kg-1, 0.4 mg·kg-1, 0.3 mg·kg-1, and 7.0 mg·kg-1, respectively, after drainage. The addition of P and HA in the early flooding stage increased the As content by 80% and 35% compared to the control, respectively, but decreased the contents of Cu, Zn, and Cd, with HA addition resulting in CaCl2-extractable Cu, Zn and Cd reduction rate > 67%. During flooding, DGT-extracted P and Fe content initially increased then decreased, while Zn content gradually reduced. The addition of P and HA significantly reduced the bioavailable Zn content in the early stages of flooding while the bioavailable content of P and As was primarily controlled by bioavailable Fe.【Conclusion】During the soil flooding-drainage incubation, significant changes occurred in soil physicochemical parameters including pH, Eh, and speciation of Fe. The addition of P and HA could regulate the bioavailability of elements such as Fe, P, and HMs. Our findings offer valuable insights for the remediation of HMs-polluted soils, highlighting the potential for using P and HA in improving soil quality and ensuring safe agricultural production.