A study was performed to compare the pharmacokinetics of major bioactive analytes in rhubarb plants to explore the pharmacological differences between raw pieces (RP) and steamed pieces (SP) of rhubarb. A rapid and efficient ultra-performance liquid chromatographic coupled with mass/mass spectrometry (UPLC-MS/MS) method was established to determine the concentrations of six analytes in rat plasma after oral administration of RP and SP. It was found that the AUC (area under the plasma concentration-time curve), Tmax (time to reach maximum plasma concentration) and Cmax (maximum plasma concentration) values were obviously increased in RP for rhein-8-O-β-d-glucophyranoside, rhein and aloe-emodin. On the contrary, emodin, physcion and chrysophanol had higher bioavailability in SP. The significant differences indicated that steamed by wine may alter pharmacokinetic behaviors of analytes, providing theoretical basis of differences in pharmacological activity between SP and RP.