The purpose of this study was to evaluate the pharmacokinetics and tissue distribution of Corydalis yanhusuo total alkaloids transdermal patch (CTTP) following Shenque acupoint application in rats. The concentrations of Corydaline (CDL), Tetrahydropalmatine (THP), Tetrahydrocolumbamine (THC), Protopine (PRO), and Dehydrocorydaline (DHC) in rat plasma and various tissues were simultaneously detected by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) after Shenque acupoint administration of CTTP. Plasma, heart, liver, spleen, lung, and kidney tissue samples were collected at specific times and separated by gradient elution on an ACQUITY UPLC HSS T3 column (1.8 μm, 100 mm×2.1 mm) with a mobile phase of 0.01% formic acid aqueous solution and acetonitrile-0.01% formic acid. The methodological results showed that the selectivity, linear range, accuracy, precision, stability, matrix effect, and extraction recovery of the established method met the requirements of biological sample analysis. The results denoted that CTTP following Shenque acupoint administration rapidly delivered adequate drug into rat blood and maintained an effective plasma level for a significantly longer time than non-acupoint administration. Furthermore, CTTP effectively reached the liver through Shenque acupoint administration and showed tissue selectivity. The data obtained could provide a prospect for the treatment of chronic pain with CTTP following Shenque acupoint application.