Wheat variety Yannong 999 (YN999) shows stably high yield potential with strong environment adaptability. Unlocking its genetic basis and key chromosomal regions underlying high yield performance will provide theoretical support for the further application. In this study, a 55K wheat SNP array was used for genotyping the YN999, its 46 derived varieties (lines) and a natural mapping population containing 243 wheat varieties (lines). The genetic effects of the key chromosomal segments undergone strong selection was elucidated. The genetic cause of high-yielding potential in YN999 was dissected based on the composition of excellent alleles underlying the three yield components. The characteristics of high thousand kernel weight were preferentially selected and present in the derived varieties (lines). Genotyping using the wheat 55K SNP array revealed that the average genetic similarity of YN999 if compared to 46 derived varieties (lines) was 86.50%. The genetic similarity in YN999 to its derived varieties (lines) of F3, F5, F6 and F7 were 84.94%, 86.19%, 86.67% and 87.65%, respectively. A total of 222 segments of YN999 with over 95% transmission rate were detected in the offspring of YN999, and the length of the segment varied from 5.04 Mb to 108.75 Mb, among which 2A contained the longest segment with high frequency selection, being 483.37Mb, and 7D contained the shortest of 13.84 Mb. A total of 135 identified QTL related to yield traits were coincided with the 222 high-frequency selection regions, with 80, 48 and 7 QTL in the A, B and D genome, respectively. A total of 1195, 268, 790 and 678 significant SNPs, which were correlated with yield per plant, kernel number per spike, 1000-grain weight and spike number per plant, respectively, were detected by single marker QTL analysis using a natural mapping population. Among those, approximately 84.02%, 51.69%, 94.18% and 13.42% alleles contributing to the higher yield performance were identified from YN999. These results indicate that YN999 has enriched the superior alleles of yield per plant and 1000-grain weight, which might be the important genetic basis for the high and stable yield in YN999. This study provided theoretical reference in application of YN999 as key parent in molecular breeding programs, and laid a foundation for identification and cloning of the genes with high yield performance.