Phenylethanoid glycosides are the bioactive components in Monochasma savatieri that primarily contains savaside A, acteoside, and isoacteoside. Pharmacological research has been comprehensive, but there have been few studies on pharmacokinetics, especially about savaside A. An ultra high performance liquid chromatography with tandem mass spectrometry with multiple reaction monitoring mode was developed and validated for the simultaneous determination of the three compounds from M. savatieri. Meanwhile, this method was fully validated and successfully applied to compare the pharmacokinetics and bioavailability following four different routes included intravenous injection, intraperitoneal injection, muscle injection, and oral administration. The results indicated that the three compounds could be rapidly absorbed within 1 h, and the main pharmacokinetic parameters showed significant differences (P < 0.05). The bioavailability of oral administration, intramuscular injection, and intraperitoneal injection did not exceed 0.2, 25, and 10%, respectively. Comparing the bioavailability, it exhibited that acteoside > isoacteoside > savaside A following the four administration routes. Notably, the isomerization position of acteoside and isoacteoside mainly occurred in the liver according to the pharmacokinetics profiles of intraperitoneal and intravenous injection, in addition, isoacteoside exhibited more structural selectivity than acteoside in vivo. It demonstrated that three compounds undergo different processes, mainly affected by the first‐pass effect and their intestinal stability is extremely poor.