A CE-MS method for rapid determination of aristolochic acid-I and aristolochic acid-II (AA-II) in traditional Chinese medicines and biological samples was described in the present paper. AA-I and AA-II can be baseline separated within 6 min by CE-MS with carboxymethyl-chitosan-coated capillary. CZE conditions including pH, concentration of buffer, applied voltage, and capillary temperature were systematically investigated, and the composition and flow rate of sheath liquid were also optimized for CE-MS. Furthermore, the CE-UV method without any additives in BGE solution was established and compared with the CE-MS method. The results showed that the two methods could achieve satisfactory separation efficiency, repeatability, and linearity, while the LOD was 0.6 mu g/mL for CE-UV and 0.05 mu g/mL for CE-MS. Compared with the CE-UV method, the sensitivity of CE-MS was significantly improved, in addition to the structure information provided by MS detection at the same time. As an application example, a spiked sample in human serum was analyzed by the CE-MS method, indicating that the new CE-MS method can be applied to analyze AAs in biological samples.