Seed desiccation is a key physiological process during plant seed maturation, directly affecting seed moisture content, storage, and quality. In agricultural practice, the kernel dehydration rate (KDR) is a critical determinant of seed water content at harvest and seed quality for mechanical harvesting. Over the past decades, although physiological changes in transcriptome and hormone levels have been linked to seed dehydration, little progress for underlying mechanisms has been achieved. A recent study identified a QTL located in a non-coding region, named qKDR1, which regulates the dehydration rate during maize seed maturation. By recruiting the transcription factors ZmMYBST1 and ZmMYBR43, it suppresses the transcription of the micropeptide-encoding gene RPG upstream of qKDR1, leading to reduced expression of RPG. The encoded micropeptide, microRPG1, regulates the KDR through the ethylene signaling pathway, highlighting its potential in crop breeding and agricultural practices. This study advances our understanding of the molecular mechanisms underlying seed desiccation and provides theoretical support for breeding crops with faster KDR and improved storage qualities.