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Soybean white mold (SWM) caused by Sclerotinia sclerotiorum is a serious disease of soybean and other plant, which is mainly distributed in the soybean producing areas of north China, east China, southwest and northeast China. The tolerance of soybean to sclerotium is partial resistance (quantitative trait), which is controlled by multiple genes. Mapping QTL and identifying candidate genes underlying soybean tolerance to SWM can accelerate the process of breeding for disease-resistant varieties. In the present study, a total of 128 lines derived from the susceptible soybean cultivar Hefeng25 and the disease tolerant soybean cultivar Maple Arrow were evaluated by in vitro and in vivo inoculation methods. A total of 78 SSR markers were used to construct linkage groups (D1a (Chr.01), A2 (Chr.08), B1 (Chr.11) and F (Chr.13)) which intensively distributed SWM resistance related QTLs. Five QTLs were detected through combining two sets of phenotypic data with the composite interval mapping (CIM) method. A total of seven candidate genes located in the five QTLs were induced by Sclerotinia sclerotiorum. The SSR markers and candidate genes associated with tolerance to Sclerotinia sclerotiorum could be helpful for SWM resistance breeding in soybean.