High-performance liquid chromatography (HPLC) with diode-array detection interfaced to atmospheric pressure chemical ionization (APCI)-mass spectrometry (MS) is applied to analyze phthalides from Chuanxiong (the rhizome of Ligusticum chuanxiong). This herb material, containing plenty of phthalide compositions, is selected as the analytical target in this paper for its hematological activity. Some of the phthalides are not stable and are difficult to analyze by gas chromatography-MS. Under optimized LC-MS-MS conditions, six phthalides in the methanol extract of Chuanxiong are unambiguously identified, and characteristic fragments are obtained using homemade reference standards. Ten other phthalides in the extract are confirmed by means of LC-APCI-MS with positive-negative ion mode and collision-induced dissociation in combination with UV spectrophotometry. The results show that LC-MS-MS is a method of choice for fast detection and detailed structural analysis of such mixtures in the crude extract of Chuanxiong.