Decreased micronutrient concentration in cereal grains caused by excessive application of phosphorus (P) fertilizer may contribute to reduce their nutritional quality. To help correct this problem in maize grain, a 3-year field experiment was conducted to determine how P application rate affects micronutrient partitioning in maize shoots and other plant organs and micronutrient bioavailability in grain. Phosphorus application significantly decreased shoot zinc (Zn) and copper (Cu) concentrations at all growth stages but had no effects on shoot iron (Fe) and manganese (Mn) concentrations. As the P application rate increased, shoot Zn and Cu contents decreased, and shoot Fe and Mn contents increased. The ratios of pre-anthesis to post-anthesis mineral contents were not affected by P application rate except Zn. P application increased the percentage of Zn that was allocated to grain and decreased the percentage that was allocated to other tissues, but had no effects on the allocation of other micronutrients among tissues. The bioavailability of Zn, Cu, Fe, and Mn in grain decreased as P application rate increased. Overall, taking account of grain yield and nutrients concentration, P fertilizer rates should range from 12.5 to 25.0 kg P ha −1 under the local condition. It can be concluded that not only grain yields, but also nutritional quality, should be considered in assessing optimal P rates in maize.