A comprehensive approach for the separation and identification of components in a traditional Chinese medicine Lobelia chinensis Lour. was developed using 2D-HPLC coupled with an online photodiode array (PDA) detector and a mass spectrometer. The extract of L. chinensis Lour. was separated on a CN column in the first-dimensional HPLC, and then each of the collected fractions was further separated on an ODS column followed by an online PDA detector. After separation in the two different chromatographic modes, the eluents were delivered to a quadrupole mass spectrometer equipped with a multimode ion source of an ESI and an atmospheric pressure chemical ionization (ESI/APCI). At least 536 components in L. chinensis Lour. extract were detected and 6 of them were identified as apigenin 7-O-rutinoside, luteolin, lobetyolinin, lobetyolin, diosmin, and linarin, respectively, according to their UV spectrum and mass spectrum. The results demonstrated the powerful resolution, high peak capacity, as well as the identification capability of the 2D-HPLC combined with PDA and ESI/APCI-MS for the analyses of complex samples.