We conducted a large-scale genome-wide association study evaluation of 683 common bean accessions, including landraces and breeding lines, grown over 3 years and in four environments across China, ranging in latitude from 18.23° to 45.75° N, with different planting dates and abiotic or biotic stresses. A total of 505 loci were associated with yield components, of which seed size, flowering time and harvest maturity traits were stable across years and environments. Some loci aligned with candidate genes controlling these traits. Yield components were observed to have strong associations with a gene-rich region on the long arm of chromosome 1. Manipulation of seed size, through selection of seed length versus seed width and height, was deemed possible, providing a genome-based means to select for important yield components. This study shows that evaluation of large germplasm collections across north-south geographic clines is useful in the detection of marker associations that determine grain yield in pulses.