Soda saline-alkali significantly hinders rice growth, phosphorus utilization efficiency, and yield formation. The application of biochar can alleviate the adverse effects of saline-alkali stress on crops. However, there is limited research on the interaction between biochar and phosphorus fertilizer concerning ionic accumulation, phosphorus utilization efficiency, and rice yield in soda saline-alkali soils. A two-year field experiment was conducted to study the combined effects of biochar and phosphate fertilizer on ionic accumulation, physiological status, phosphorus utilization efficiency, and rice yield in soda saline-alkali soil. Four treatments were established for the study: NK (225 kg N, 75 kg K ha−1 year−1), NPK (225 kg N, 70 kg P, 75 kg K ha−1 year−1), NK + B [225 kg N, 75 kg K ha−1 year−1, 1.5% biochar (w/w)], and NPK + B [225 kg N, 70 kg P, 75 kg K ha−1 year−1, 1.5% biochar (w/w)]. The findings indicated that the combined application of biochar and phosphorus fertilizer (NPK + B) significantly reduced the Na+ concentration, Na+/K+ ratio, malondialdehyde (MDA), superoxide anion (O2−), and hydrogen peroxide (H2O2) levels in rice plants. Furthermore, it resulted in a significant increase in K+ concentration and elevated the levels of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), proline (Pro), soluble protein (SP), soluble sugar (SS), and acid phosphatase (ACP). The NPK + B treatment exhibited a significant difference compared to the other treatments (p < 0.05). Compared with NK, phosphorus accumulation and phosphorus utilization efficiency under NPK + B were significantly increased (p < 0.05). The average of biomass yield, grain yield, and harvest index of NPK + B, NK + B, and NPK significantly surpassed those of NK by 6.28–12.25%, 19.80–42.13%, and 11.59–24.64%, respectively. Moreover, a significant difference was observed between NPK + B and the other treatments (p < 0.05). Principal component analysis of the two-year mean data revealed a strong positive correlation of 89.5% for PC1 and a minor negative correlation of 4.4% for PC2. Our research findings demonstrate that the combination of biochar and phosphorus fertilizer effectively enhances salt and alkali tolerance in rice plants, resulting in increased yield through improved ionic balance and physiological status.