Taking three rapeseed (Brassica napus L.) with different waterlogging tolerance as the control, waterlogging tolerance of 15 stable lines between Brassica napus and Rorippa indica were identified and evaluated comprehensively in seedling period by using simulated drought in plastic pots. The results showed that: (1) waterlogging restrained root system growth, resulting in shorter plant, yellow leaves and biomass decreased. Effects of waterlogging on root system were most serious compaired to the plant total biomass and the growth of plant upside. (2) Through principal components analysis and subordinate function analysis, 10 character indexes, including number of leaves, ratio of green leaves, seedling height, root length, fresh weight of plant upside, root and the whole plant, dry weight of plant upside, root and the whole plant, were transformed into a single comprehensive evaluation value (D value), which accurately provided comprehensive evaluation for 18 materials, also provided method reference for Brassica napus waterlogging tolerance evaluation in seedling period. (3) Waterlogging tolerance coefficient of 9 character indexes (excluding ratio of green leaves) from 15 innovative germplasm all were higher than the control cultivars. Comprehensive evaluation results showed D value of 15 germplasm all were higher than Yuhuang No.2, D value of 13 germplasm were higher than Zhongyou 821 with high comprehensive tolerance and D value of 3 germplasm were higher than Zhongshuang No.9 with high waterlogging tolerance. Cluster analysis showed innovative germplasm accounted for 6 (85.71%) in 7 germplasm with high waterlogging tolerance. Consequently, the waterlogging tolerance of innovative germplasm were higher than the control cultivars averagely, which indicated that innovative germplasm from wide cross obviously improved waterlogging tolerance of Brassica napus.