The Zn content in cereal seeds is an important trait for crop production as well as for human health. However, little is known about how Zn is loaded to plant seeds. Here, through a genome‐wide association study (GWAS), we identify the Zn‐NA (nicotianamine) transporter gene ZmYSL2 that is responsible for loading Zn to maize kernels. High promoter sequence variation in ZmYSL2 most likely drives the natural variation in Zn concentrations in maize kernels. ZmYSL2 is specifically localized on the plasma membrane facing the maternal tissue of the basal endosperm transfer cell layer (BETL) and functions in loading Zn‐NA into the BETL. Overexpression of ZmYSL2 increases the Zn concentration in the kernels by 31.6%, which achieves the goal of Zn biofortification of maize. These findings resolve the mystery underlying the loading of Zn into plant seeds, providing an efficient strategy for breeding or engineering maize varieties with enriched Zn nutrition. Synopsis The metal‐NA (Nicotianamine) transporter ZmYSL2 loads Zn from the maternal tissue into maize kernels. Overexpression of ZmYSL2 increases the amount of Zn in maize kernels, providing a potential approach for breeding Zn‐rich crop. Polymorphisms in basal endosperm transfer cell layer (BETL) localized ZmYSL2 correlate with natural variations in the Zn concentration of maize kernels. The opaque phenotype of ZmYSL2 mutants is due to deficiency of Zn rather than Fe in the kernels. Overexpression of ZmYSL2 increases the Zn concentration in the kernels by 31.6%, which achieves the goal of Zn biofortification of maize. The metal‐NA (Nicotianamine) transporter ZmYSL2 loads Zn from the maternal tissue into maize kernels. Overexpression of ZmYSL2 increases the amount of Zn in maize kernels, providing a potential approach for breeding Zn‐rich crop.