Abstract: Two rapeseed (Brassica napus　L.) varieties (Zhongshuang No.10 and Zhongyouza No.5) were used to study the effects of application of nitrogen (N), phosphorus (P) and potassium (K) fertilizers on yield in rapeseed under the waterlogging stress. The plant was submerged at the seedling stage to mimic the condition of waterlogging. The experiment was replicated two times with “3414” design. The results showed that N, P and K fertilization significantly affected yield traits in rapeseed under the waterlogging stress. The grey relational analysis showed that N application rate was positively correlated with the number of seed per pod, siliques per plant, primary branches, secondary branches and the length of raceme. The P application rate was positive correlated with the number of siliques per plant and seed per pod. And K application rate was positive correlated with the number of seed per pod, 1000-seed weight and the length of raceme. The results indicated that the ensuring middle level of P and K fertilization, enhanced nitrogen fertilization can significantly increase the yield of rapeseed and the cost value ratio and economic benefits under waterlogging stress. By establishing the fertilizer response equations, the optimum fertilizer applicant of rapeseed under the waterlogging stress were as N 267 kg/ha, P2O5 120 kg/ha, K2O 120 kg/ha.