The hidden hunger caused by grain zinc (Zn) deficiency in crop poses a potential threat to the health of nearly two billion people worldwide, especially in developing countries. In this study, the long-term phosphorus fertilizer experiment and in vitro detached rice panicle culture systems with varied phosphorus levels were conducted to investigate the effect of phosphorus on rice grain Zn bioavailability and its relation of grain inositol phosphates profiles (phytic acid related metabolic derivatives) concentration. In our results, compared with low phosphorus level, high phosphorus supply increased grain phytic acid phosphorus and total phosphorus concentration (mg g–1). Moreover, high phosphorus supply also increased different grain inositol phosphate profile concentrations (InsP1-6), especially for InsP4-6. On the contrary, grain Zn concentration decreased with phosphorus supply. Both the decrement of Zn and increment of phytic acid phosphorus induced by the higher phosphorus supply in rice grain led to the significant decrement of grain Zn bioavailability. In in vitro detached panicle culture system, the Zn bioavailability in P12 treatment decreased by 81.3% relative to P0 treatment. In conclusion, higher phosphorus input could significantly decrease grain Zn bioavailability through increased grain phytic acid phosphorus and inositol phosphates derivatives concentration, in addition to the decrement of grain Zn concentration.