Improving the management of water and fertilizers is an effective method for enhancing the seed-setting performance of rice. This study aimed to explore the regulation of optimized water and nitrogen management on the root-leaf hormone balance and seed-setting performance of drip-irrigated rice. In a 2-year field experiment, T-43 (a drought-resistant cultivar) and LX-3 (a drought-sensitive cultivar) were cultivated under two drip irrigation treatments (W-1, limited, and W-2, deficit) and three nitrogen fertilization treatments (N-1, seedling:tillering:panicle:grain-filling, 30%:50%:13%:7%; N-2, 20%:40%:30%:10%; and N-3, 10%:30%:40%:20%). Compared with other treatments, the W1N2 treatment increased the seed-setting rate and grain biomass accumulation (2.7%-9.2% and 4.5%-69.8%) of the two cultivars on the basis of producing a higher effective panicle number, and T-43 had a much higher seed-setting rate and yield than LX-3 (6.8%-14.6%). Increased fertilizer applications at the panicle and grain-filling stages (N-2) enhanced the root oxidation activity (ROA) and the zeatin+zeatin riboside (Z + ZR) and gibberellic acid (GA(3)) contents in the roots in the 0-10 cm layer and in the leaves from the heading stage to 20 days after heading. The grain biomass accumulation of T-43 was significantly positively correlated with abscisic acid (ABA) and Z + ZR in the roots and leaves, while the grain biomass accumulation of LX-3 was significantly positively correlated with auxin, ABA, Z + ZR/ABA, and GA(3)/ABA in the roots in the 10-20 cm layer. Overall, W1N2 promoted grain biomass accumulation by modulating the Z + ZR and ABA balance in roots and leaves, improved the root-shoot ratio, and enhanced ROA, thereby improving the seed-setting performance of drip-irrigated T-43 rice.