Cross combinations from six rapeseed cultivars and lines were evaluated under waterlogging stress condition in order to understand the genetic mechanism of waterlogging tolerance of Brassica napus L. and provide reasonable improvement programs. There were six gemination traits investigated on combining ability and heritability using complete diallel crossing method designed for 30 combinations from those six cultivars and lines. The traits included relative root length,stem length, fresh weight per plant, survival rate, electrical conductivity, and vigor index. After flooding treatment, the six traits of parents and F1 were analyzed. The general combining ability (GCA) and special combining ability (SCA) of gemination traits were analyzed using Griffing I method. Among 30 cross combinations, the GCA was significantly different among six waterlogging resistance traits. The SCA of these traits was significantly different except the SCA of electrical conductivity. As a representative trait of waterlogging tolerance in rapeseed, relative vigor index had the highest narrow heritability and relatively low broad heritability. The cultivars Zhongshuang 9 and P79 had higher tolerance potential to waterlogging stress. It can be concluded that combining ability and genetic effects of relative vigor index during germination stage could be used to identify the waterlogging tolerance of rapeseed in breeding program.