A comprehensive two-dimensional liquid chromatographic (2D-LC) separation system based on the combination of a CN column and a Merck Chromolith Flash reversed-phase column was developed for the separation of components in Adinandra nitida, one type of traditional Chinese medicine (TCM). The two dimensions were connected by a ten-port, dual-position valve controlled automatically by software written in-house. The effluents were detected by both ultraviolet and atmospheric pressure chemical ionization source ion trap tandem mass spectrometry (MS). The calculated peak capacity of the 2D-LC-MS/MS system was above 1240. More than 57 components were resolved in the methanol extract from Adinandra nitida leaves, and five of these were identified based on their relative retention times, molecular weights and MS/MS spectra.