A rapid and sensitive hydrophilic interaction liquid chromatography method was developed for the identification and quantitative determination of 17 nucleosides and nucleobases by using ultra-high performance liquid chromatography separation system coupled to triple quadrupole mass spectrometer. Sufficient separation of the target compounds was achieved on an Acquity BEH Amide column (2.1 mm × 100 mm, 1.7 μm) in a single run of 9 min. The LOD and LOQ were in the range of 0.017–50.00 ng ml−1 and 0.056–146.00 ng ml−1, respectively. Then, the method was applied for the analysis of nucleosides and nucleobases in Elaphuri Davidiani Cornu and Cervi Cornu. Multivariate statistical analysis was also used to investigate the differences in the nucleosides and nucleobases profiles among the samples. The present study also provided helpful information for quality control of Elaphuri Davidiani Cornu and Cervi Cornu.