As one of the most widely promoted effective irrigation strategies for rice, alternate wetting and drying (AWD) irrigation can not only reduce water use but also increase mineral nutrient use efficiency. In this research, we compared the differences in grain yield, grain quality, phosphorus use efficiency (PUE), and growth states of roots and shoots of lowland and upland rice cultivars that were subjected to different irrigation and phosphorus (P) fertilizer application treatments in a field study for two years. The irrigation treatments consisted of two irrigation regimes: continuously flooded (CF) and AWD irrigation and the P fertilizer treatments included three P rates, i.e., 0, 45, and 90 kg ha−1 (P0, P45, and P90, respectively). The results revealed that AWD irrigation led to an increase in grain yield and improved PUE of both rice varieties at P45. The roots were longer and deeper under AWD irrigation, which contributed to the higher grain yield and higher resource use efficiency obtained with this treatment. At the lower P rates, both rice types translocated more P from vegetative tissues to grains, which led to a better PUE. Molecular analysis show that plant hormones (IAA, gibberellins, cytokinins and ABA) and members of the OsPht1 family are also involved in the regulation of P homeostasis under AWD irrigation. Our results demonstrate that AWD irrigation can also enhance PUE for the rice in the field.