Cytokinins are important plant hormones that regulate plant growth and development, while vigorous growth usually requires a matching nutrient supply. In agriculture, cytokinins have been used for crop yield improvement via modulating cytokinin metabolism, but little is known about how to manipulate cytokinin allocation to improve effectual utilization of nitrogen within plants to increase crop productivity. Here, we identified a novel cytokinin transporter INCREASED GRAIN NUMBER1 (IGN1) that regulates grain yield in rice through a genome-wide association study. Further study revealed that IGN1 acts as a novel type of cytokinin transporter and promotes the translocation of cytokinin iPR into panicles, subsequently directs nitrate distribution in panicles through regulating the expression of OsNPF genes. More importantly, we demonstrated that IGN1 is able to enhance the redistribution of nitrate from leaves (source) to panicles (sink) in response to the nitrogen status, thereby maximizing the utilization of nitrogen in planta to increase rice panicle size. Moreover, the application of SP1 beneficial alleles can increase the effective allocation of cytokinin and nitrate to panicles, by which nitrogen use efficiency (NUE) and rice yields are significantly improved in the field. Taken together, our results not only reveal a novel mechanism on cytokinin-nitrogen synergy involved in the regulation of important agronomic traits, but also provide an applicable genetic target for cultivating high-yielding and high-efficiency rice varieties.