Hydroxyapatite (HA) is often applied as chemical amendment in soils contaminated with trace metals such as copper (Cu) and cadmium (Cd). Large amounts of iron oxides in red soil may interacts with phosphate released from HA and influence trace metal immobilization of HA. Here we simulated a red paddy soil with 1–5% wt iron oxides by adding hematite and evaluated the Cu and Cd availability in soil amended with HA under flooded conditions. Changes in phosphorus and iron oxide fractions were also evaluated after a 42-day flooding incubation experiment. Results showed that the addition of HA-only and hematite-only decreased soil redox potential and increased pore water pH compared to the control. HA combined with hematite could effectively decrease phosphate, Cu and Cd in soil pore water compared to HA-only. Additionally, HA combined with hematite could also increase soil pH and decrease soil CaCl2-extractable Cu and Cd. In particular, HA combined with 5% hematite was most effective in reducing soil exchangeable fractions of Cu and Cd by 53.7% and 65.6% compared to the control, respectively. The addition of HA-only increased water-soluble phosphorus, NaHCO3-extractable inorganic phosphorus, NaOH-extractable inorganic phosphorus, and HCl-extractable phosphorus. Conversely, HA combined with hematite treatments decreased NaHCO3-extractable inorganic phosphorus by 11.3–43.0% compared to HA-only. Vivianite and metal–phosphate precipitates were not observed using the Visual MINTEQ model, X-ray diffraction, and chemical analysis. The addition of hematite with or without HA increased free and crystal iron oxide fractions, while it substantially enhanced amorphous iron oxides in the soil. Thus, this study indicates that soil with high hematite content could enhance Cu and Cd immobilization while decreasing phosphorus availability in the red paddy soil amended with HA under the flooded conditions.