A field experiment with 24 different treatments was carried out to study the effects of a combination of water management (WM), soil application of calcium magnesium phosphate (CMP), and foliar spraying of Si/Se on Cd uptake by paddy rice (Teyou 524). The water management modes included W₁ (conventional water management) and W₂ (flooding during the whole growth period). The application of CMP included P₁ (1800 kg·hm⁻²) and P₂ (3000 kg·hm⁻²). The leaf spraying regulations included LS (2.0 mmol·L⁻¹ Na₂SiO₃), LX (25 μmol·L⁻¹ Na₂SeO₃), and LSX (1.0 mmol·L⁻¹ Na₂SiO₃ and 12.5 μmol·L⁻¹ Na₂SeO₃). The results indicated that, compared to the control (W₁), flooding and CMP reduced soil exchangeable Cd by 10.3, 21.5, 32.2, 27.6 and 36.9% under conditions of W₂, P₁, P₂, W₂P₁ and W₂P₂, respectively; but the grain yield was reduced under W₂ condition. Some individual treatments, including W₂, P₁, P₂, LS, LX, and LSX, could reduce Cd concentration in the grain by 23.1–60.3%; but the combined regulations could reduce grain Cd concentrations up to 79.5%. Only the combined mode of CMP and leaf spraying of Si/Se could control grain Cd concentration below the Chinese National Food Safety Standard (0.2 mg·kg⁻¹). Combined modes of fertilizer application (W₂ and CMP) and foliar spraying (Si/Se), including W₂P₂LS, W₂P₂LX, W₂P₂LSX, were the most effective in reducing the Cd transport coefficients of both root-to-straw (RS) and straw-to-seed (SS). Considering Cd concentration in grain, treatments W₂P₂LS and W₂P₂LSX were the most effective ones, which could reduce Cd concentrations to 0.090 mg·kg⁻¹ and 0.089 mg·kg⁻¹ in grain, respectively. These results demonstrated that combined manipulation of the root zone (W₂ and CMP) and foliar spraying (Si/Se) can effectively reduce grain Cd concentrations in rice.