To evaluate the differences of Ophiopogonjaponicus from different cultivations, the metabolomics based method was conducted to compare the effects of Hangmaidong and Chuanmaidong (Chinese name) on plasma endogenous metabolites of normal rats. Data were collected by ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-Q-TOF/MS), and were analyzed by multivariate statistical method, such as Principal Component Analysis and Orthogonal Signal Correction Partial Least Square Discriminant Analysis. Results revealed that the plasma metabolites profiling of low and middle dose group of Chuanmaidong were similar to the control group, but different from the high dose group obviously. Meanwhile the high, middle and low dose groups of Hangmaidong were different from control group notably, and the difference is dose dependent. Lysophosphatidylcholines, the possible endogenous metabolites which contribute to the classification most significantly, are closely related to cardiovascular system diseases. Compared with the group of Chuanmaidong, Hangmaidong has greater impact on the plasma metabolic profiling of normal rats. Hangmaidong and Chuanmaidong showed significant differences pharmacodynamically.