Zhongmian 113 overcomes the genetic trade-off between growth duration, yield, and quality, reducing planting risks in northwestern inland areas. Using advanced technologies (PacBio HiFi, ONT ultra-long-read sequencing, Hi-C), we assembled its telomere-to-telomere gap-free genome and elucidated the genetic basis of its superior traits . Based on the ZM113 reference genome, a combined genome-wide association study (GWAS) on 419 core cultivated germplasms and haplotype analysis of 229 wild/semi-wild resources identified an excellent early-maturing haplotype, GhEF-D03early, on chromosome D03. This segment is a recombination-suppressed region with linkage disequilibrium (LD) spanning over 10 Mb, driven by a large pericentric inversion. Within this interval, numerous candidate genes related to early flowering and photoperiod regulation are fixed in a “super-gene” configuration. Further analysis showed the D03_INV inversion is fixed in cultivated cotton populations but absent in most landraces .