Edible waxy maize is a unique domesticated cereal valued for its superior sensory and nutritional properties, yet high-quality gap-free genomes remain lacking, hindering the exploration of structural variations (SVs) and domestication-related divergence. Here, we assembled two chromosome-level, gap-free genomes of the elite waxy maize inbred lines Tongxi 5 and Hengbai 522, the parents of the widely cultivated hybrid Suyunuo 1. Comparative genomic analysis revealed substantial genome size variation, prominent megabase-scale SVs, and extensive knob-repeat expansion in Tongxi 5. We identified widespread gene presence–absence variation and hyperdivergent regions enriched in transposable elements, which largely underpin genomic differentiation between waxy and field maize. Population genomic analyses further demonstrated asymmetric introgression from field maize into the two parents, whereas the conserved waxy haplotype supports a shared ancestral origin. Integrative GWAS based on SNPs, InDels and SVs revealed that SVs substantially contribute to phenotypic diversity and mediate the co-regulation of yield traits and flavor-related metabolites. Our results uncover key genomic events underlying post-domestication divergence and highlight the essential roles of SVs in heterosis and flavor–yield balance, providing valuable genomic resources for waxy maize improvement.