The wheat landrace Xiaoganmai (ZM011362), originating from Dangyang, Hubei Province, exhibits multiple desirable traits, including multi-floret and high-grain-number characteristics, numerous effective tillers, stable pre-harvest sprouting resistance, and adult-plant resistance to stripe rust, making it a potentially valuable germplasm resource for modern wheat breeding. In a previous study, 178 Shumai 753/Xiaoganmai-derived lines were developed using Xiaoganmai as the donor parent and the elite breeding line Shumai 753, which carries all-stage stripe rust resistance genes and shows good overall agronomic performance, as the recurrent parent through hybridization, backcrossing, continuous multi-generation selfing, and a segmented target-trait selection strategy. This study aimed to dissect the genetic basis of the Shumai 753/Xiaoganmai-derived lines at the molecular level, identify key chromosomal regions controlling yield, disease resistance, and stress tolerance, and provide molecular evidence for the genetic improvement of wheat using landraces. Whole-genome scans of Xiaoganmai, Shumai 753, and their 178 derivative lines were performed using the wheat 55K liquid SNP array, and a total of 52,779 valid homozygous polymorphic SNP loci were obtained. Genetic similarity and genetic composition of the parents and derivative lines were analyzed based on these polymorphic SNP loci. The genetic similarity coefficient between the two parents was only 0.44, indicating substantial genetic divergence between Xiaoganmai and Shumai 753 at the molecular level. Analysis of the genetic similarity and composition of the derivative lines showed that their whole-genome molecular profiles were largely consistent with their pedigree background, with no obvious bias in parental inheritance. Based on marker-trait genome-wide association analysis, 127 chromosomal regions or loci significantly associated with plant height (14), spike length (12), spikelet number per spike (21), effective tiller number (20), thousand-grain weight (25), and relative seed germination index (35) were identified. Analysis of parental genetic contributions revealed that the proportions of SNP loci inherited from Xiaoganmai and Shumai 753 in the derivative lines ranged from 7.88% to 43.95% and from 56.05% to 92.12%, with average proportions of 26.45% and 73.55%, respectively. In total, 86 and 259 high-frequency selected regions derived from Xiaoganmai and Shumai 753, respectively, with sizes ranging from 0.01 to 108.75 Mb and contribution rates ≥80%, were identified in the derivative lines and were unevenly distributed across the 21 wheat chromosomes. Combined with the genome-wide association mapping results, 43 high-frequency selected chromosomal regions derived from Xiaoganmai and Shumai 753 were significantly associated with plant height, spike length, spikelet number per spike, effective tiller number, thousand-grain weight, and relative seed germination index. Among these regions, 16 simultaneously controlled two or more traits, indicating pleiotropic effects. Further analysis of the genetic composition of high-frequency selected chromosomal regions in 14 elite derivative lines revealed that the preferential transmission of regions significantly associated with important yield-related traits, together with their targeted selection as key loci, underlies the successful utilization of the landrace Xiaoganmai to improve the yield structure of Shumai 753 and ultimately achieve coordinated improvement in yield, disease resistance, and stress tolerance.