You-Gui-Yin (YGY), a famous traditional Chinese medicine, has been widely used in clinics for the treatment of kidney-yang deficiency, yang deficiency caused by excessive yin, and osteoporosis. A rapid and sensitive ultraperformance liquid chromatography–electrospray ionization–mass spectrometry (UPLC–ESI–MS) method for simultaneous determination of six Aconitum alkaloids including aconitine (AC), hypaconitine (HA), mesaconitine (MA), benzoylaconine (BAC), benzoylhypaconine (BHA), and benzoylmesaconine (BMA) in rat plasma after oral administration of YGY was developed in this study. Chromatographic separation was performed on an ACQUITY UPLC™ BEH C18 column (2.1 × 100 mm, 1.7 μm) using gradient elution with the mobile phase consisting of 2 mmol/L ammonium formate in 0.05% formic acid aqueous solution and 0.05% formic acid methanol solution, at a flow rate of 0.20 mL/min. MS detection was performed in the positive ion mode. The calibration curves were linear in the concentration range of 0.04160–41.60 ng/mL, 0.1070–107.0 ng/mL, 0.07358–73.50 ng/mL, 0.03228–32.28 ng/mL, 0.01809–18.09 ng/mL, and 0.1320–132.0 ng/mL for AC, HA, MA, BAC, BHA, and BMA, respectively. The intra- and inter-day precisions (relative standard deviation [RSD]) were less than 11.6% and 12.6%, respectively. The accuracies Relative Error (RE) ranged from −10.2% to 5.6%, while the recoveries ranged from 70.4% to 99.3%. The method for simultaneous quantitation of Aconitum alkaloids of You-Gui-Yin in rat plasma is accurate and repeatable, and this method was successfully applied to investigate the pharmacokinetics of the six Aconitum alkaloids in rat plasma after oral administration of YGY. For the pharmacokinetic study, the pharmacokinetics of the six Aconitum alkaloids were best described by a two-compartment open model.