Staple crops such as rice, wheat and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches and rational design strategies presents opportunities to develop high-yield “super-crop” varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.