AbstractXanthii fructus (XF), the fruit of Xanthium sibiricum Patr., is a traditional Chinese materia medica commonly used to treat allergic rhinitis and other rhinitis diseases. To uncover the mechanism of the stir‐frying process and its effect on the pharmacokinetic behavior of active compounds in model rats, four active compounds—chlorogenic acid, 4‐caffeoylquinic acid, 1,5‐O‐dicaffeoylquinic acid and apigenin—were selected based on previous spectrum‐effect experiments. High performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC–QqQ–MS) technology, an accurate and feasible method, was applied to measure the concentration of these four compounds in rat plasma. This validated method can accurately measure the concentration of each compound at each sampling point of rat plasma. This validated method shows good linearity, extraction recoveries, matrix effects, intra‐ and inter‐day precision and stabilities. Compared with the XF group, the maximum plasma concentration (Cmax) value of 1,5‐O‐dicaffeoylquinic acid decreased remarkably (p < 0.05) after oral administration of stir‐fried Xanthii fructus (SXF) extract, while the other compounds showed no significant difference. The mean residence time value of chlorogenic acid (p < 0.05) and 1,5‐O‐dicaffeoylquinic acid (p<0.01) after oral administration of SXF extraction demonstrated significant differences compared with the XF group, while the other two compounds showed no statistical difference, indicating that the stir‐frying process prolonged the effect time and delayed the removal time of chlorogenic acid and 1,5‐O‐dicaffeoylquinic acid. The values of the area under the plasma concentration–time curve from zero to the last quantifiable time‐point, the area under the plasma concentration–time curve from zero to infinity, the time to maximum concentration and the elimination half‐life of four compounds in the SXF group showed no statistically significant difference from the XF group. From this data, we speculated that the stir‐frying process can not only keep the absorption of 4‐caffeoylquinic acid and apigenin, but also increase the effect time of chlorogenic acid and 1,5‐O‐dicaffeoylquinic acid, which could be the mechanism underlying the stir‐frying process enhancing the effects of XF.