AbstractOrganic fertilization is considered an effective approach in promoting agricultural green development, dramatically affecting soil phosphorus (P) availability. Nonetheless, limited information is available on the comprehensive impact of full substitution of organic fertilizer for chemical fertilizer on P speciation, phytoavailability, and apparent balance throughout different rice‐growth stages. To address this gap, a 5‐year field experiment was conducted, implementing five organic P gradients ranging from 0 (P0), 70 (P70), 140 (P140), 210 (P210) to 280 (P280) kg P2O5 ha−1 of organic fertilizer. To assess P phytoavailability in the root zone with submillimetre spatial resolutions, this study employed techniques such as the one‐ and two‐dimensional diffusive gradients in thin films (DGT) technique and the high‐resolution soil solution sampling technology (HR‐Peeper). The findings revealed that increasing P rates enhanced soil Olsen‐P and biological‐based P fractions across rice‐growth stages, primarily driven by variation in mineral‐associated P. Notably, the P140 treatment demonstrated the highest P uptake efficiency among the different rice‐growth stages, with a significant increase in soil DGT‐P, particularly in the 0–60 mm soil layer (p <0.05), providing tangible evidence for enhanced P uptake. Moreover, compared with higher P treatments (P210 and P280), the P140 treatment markedly increased P use efficiency by 31.7% and 99.0%, respectively (p <0.05). Further, with a high ratio of DGT‐P to Peeper‐P and a low apparent balance of P, organic fertilization at the rate of 140 kg P2O5 ha−1 effectively struck a balance between ensuring adequate P supply for yield stability and mitigating potential P loss risks. These results underscore the significance of optimal organic fertilization in enhancing agronomic benefits while reducing environmental risks. They offer valuable insights to support field P management strategies and government decision‐making processes.