ABSTRACT Seed vigor underpins uniform crop establishment, but its dynamic genetics are understudied. Combining high‐resolution temporal phenotyping and genomics in upland cotton, we used the SeedRanger platform to record 17 image‐based traits every 30 min over 120 h, revealing stage‐specific heritability and identifying 541 seed‐vigor loci. These loci show extensive pleiotropy and temporal coordination, forming a genetic network that preserves developmental continuity; 8.9% overlap regions under domestication selection, indicating concurrent optimization with fiber yield. Functional validation of FLA2 , a candidate gene underlying a dynamic QTL, implicates auxin‐mediated control of radicle elongation and cotyledon development. This temporal framework exposes dynamic genetic architecture and breeding targets for high‐vigor crops.