Plasma membrane (PM) vesicles were isolated from developing embryos of wheat (Triticum aestivum L.) with different drought-tolerance under drought stress by the gradient centrifugation method. The activity of the PM H+-ATPase (EC 3.6.1.35) and contents of polyamine conjugated (covalently and noncovalently) to the PM vesicles were investigated. Results showed that after drought treatment for 3 d, embryo relative water content (ERWC), embryo relative dry weight increase rate (ERDWIR) of drought-sensitive Yumai No. 48 cultivar decreased more significantly than those of drought-tolerant Luomai No. 22 cultivar, while PM H+-ATPase activity, noncovalently conjugated (NCC) spermidine (Spd) and NCC spermine (Spm), the covalently conjugated (CC) putrescine (Put) and CC Spd of PM from Luomai No. 22 cultivar increased more obviously than those from Yumai No. 48 cultivar. As judged by increases in ERWC and ERDWIR, treatment with exogenous Spd alleviated markedly drought injuries to Yumai No. 48, coupled with significant increases in NCC Spd and NCC Spm levels and H+-ATPase activity in the embryo PM vesicle. Under drought stress, the treatment of drought-tolerant Luomai No. 22 cultivar with methylglyoxyl-bis (guanylhydrazone) (MGBG), an inhibitor of S-adenosylmethionine decarboxylase (SAMDC), and phenanthrolin (o−Phen), an inhibitor of transglutaminase (TGase) respectively, caused a decrease of the NCC Spd, NCC Spm, CC Put and CC Spd. Those decreases were associated with decreased PM-H+-ATPase activity and the tolerance of developing wheat embryos to osmotic stress, as judged by decreases in ERWC and ERDWIR. These results suggest that tolerance of the developing wheat embryos to drought stress is associated with the embryo PM H+-ATPase and the levels of NCC Spd, NCC Spm, CC Put and CC Spd in embryo PM vesicles.