Winter rapeseed (Brassica napus L.) in paddy fields often suffers from waterlogging stress. This study evaluated 353 rapeseed Germplasm resources subjected to 12h waterlogging stress during the germination stage. The electrical conductivity of the soaking solution was measured, and six parameters—root length, root weight, shoot weight, etc.—were recorded after 7d of recovery growth, with untreated samples serving as controls. Comprehensive evaluation was performed using membership function analysis, principal component analysis (PCA), and cluster analysis, integrated with unit electricity conductivity. The aim was to screen for waterlogging-tolerant Germplasm resources at the germination stage. Results revealed that roots were most significantly affected by waterlogging stress during germination. Relative root length and relative root weight were identified as reliable evaluation indices for waterlogging tolerance, while unit electricity conductivity served as an auxiliary indicator. Based on comprehensive evaluation values (D-values) and conductivity per unit, the tested materials were classified into 4 types: highly tolerant, tolerant, sensitive, and highly sensitive. 6 waterlogging-tolerant Germplasm resources were identified, including Ningza 2009 and 10-Jiangpeng 3, These highly tolerant germplasms provide valuable genetic resources for breeding waterlogging-resistant rapeseeds and lay the foundation for further research on waterlogging tolerance at the seedling and flowering stages