A method was developed for the simultaneous identification of astragalosides (AGs) and isoflavonoids (IFs) in the roots of Astragalus membranaceus and Astragalus mongholicus by HPLC coupled with atmospheric pressure chemical ionization MS/MS (HPLC-APCI-MS/MS). Diagnostic fragment ions of AGs and different group of IFs were obtained with one AG and eight IF standards analyzed by CID-MS, which were adopted as characteristic MS/MS fingerprints for further identification of these compounds in the two Astragalus species by using HPLC-APCI-MS/MS. A total of 20 IFs and 10 AGs were identified or tentatively identified. Among them, six IFs were detected in A. membranaceus for the first time and five IFs were firstly identified in A. mongholicus. The results indicate that HPLC-APCI-MS/MS is a powerful tool for the simultaneous characterization of IFs and AGs in complex matrix.