Ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) is an effective technique for analysis of complex samples with offering rapid, efficient separation in combination with accurate mass measurement and tandem mass spectrometry (MS/MS). This paper exploits this technique to identify the alkaloids in corydalis yanhusuo, an important antalgic Traditional Chinese Medicine (TCM). The mass spectral fragmentation behavior of one tertiary alkaloid and two quaternary alkaloids was studied in detail. Low-abundance product ions of tertiary and quaternary alkaloids were investigated and compared between each other. Sixteen alkaloids were screened out by using a systematic screening method developed in our laboratory; structures of eight therein were identified by characteristic UV absorption spectrum and positive ion mode of Q-TOF-MS/MS; and two of them were discovered for the first time in corydalis yanhusuo to our knowledge. This research demonstrates the potential of UPLC-Q-TOF-MS in structural characterization and identification of components in traditional Chinese herbal medicines.