Many important agronomic traits of soybean are quantitative traits, which are controlled by polygenes. Tagging QTL for these quantitative traits is a very important field in soybean quantitative genetics research. Kexin 3 and Zhonghuang 20 are releasing cultivars in Huanghuaixia ecological district with excellent quality traits. A cross of Kexin 3 and Zhonghuang 20 was made, then selfed to construct F 2 population which has 192 plants. A genetic linkage group of soybean genome was constructed, which consisted 33 linkage groups with 122 SSR markers covering 1719 6 cM. The composite interval mapping was used to identify quantitative trait loci (QTL) associated with plant height, nod number of main stem and protein content. Two QTL were found for plant height with the phenotypic variance explained of 9 15% and 6 08% respectively; two for nods number of main stem with the phenofypic variance explained of 10 1% and 8 6% respectively; one for protein content with the phenotypic variance explained of 9 8%. Six markers linked to the QTL for four agronomic traits were found and can be used in molecular marker assisted selection in soybean.