The middle and lower reaches of Yangtze River is a main producing region of canola(Brassica napus L.) in China. However, canola in this region is subjected to water-logging during planting period to reduce yield. It is of importance to study the inheritance of water-logging tolerance for canola. In this paper a family lines population of six generations of P1, F1, P2, B1:2, B2:2, F2:3 derived from the cross of WR-4(resistant)×WR-5(non-resistant) was used to analyse genetic segregation by applying major gene plus polygene mixed inheritance model. The seedling mortality was recorded on the 7th day after logging-removing for plant recovery following six days full-submergence treatment of the seedlings in 2012 and 2013. The results showed that the seedling mortality was respectively fitted the genetic model of E-0 and B-3, i.e., two pairs of additive- dominant-epistatic major gene plus additive-dominant-epistatic polygene model and two pairs of additive major genes model. This result confirms that water-logging tolerance of seedling in this cross is controlled mainly by two major genes which expressed in the mode of additive-dominantepistatic effects. While dominant effects expressed(2012) it gave a higher value of |h a|=0.3475, |h b|=0.0069 than the additive effect of the major genes which was |d a|=|d b|=0.0036. In the populations of B1:2, B2:2, and F2:3, h2 mg was 36.25%, 61.40%, and 61.84%, respectively, with an average of 53.16% in 2012, and 8.30%, 30.48%, and 43.13%, respectively, with an average of 27.30% in 2013. Variance from environment effects was 59.77% of the total phenotypic variance on an average in two years. A conclusion could be made that water-logging tolerance of seedling in B. napus is controlled by two major genes but heavily af-fected by environment. Since a higher value of h2 mg was detected in F2:3 populations, selection in early generations might be an effective way for waterlogging tolerance breeding in B. napus.