The focus of this study was the analysis of the complex chemical composition from different parts of Buddleja davidii, whose species are commonly known as ornamental plants and herbal medicines in many countries. As an herbal medicine, it has been utilized for stroke treatments, headache, wound healing, neurological disorder, etc. However, the understanding of its chemical matrices is still insufficient. Therefore, an online two-dimensional reversed phase liquid chromatography x hydrophilic interaction liquid chromatography (RPLCxHILIC) system coupled with mass spectrometry was applied for further detailed investigation of the chemical constituents in Buddleja dividii. In this two-dimensional liquid chromatography (2D-LC) method, a new at-column dilution (ACD) modulator was introduced in the 2D-LC system to solve the incompatibility problem of the mobile phase between two dimensions, which resulted in a 2D-LC analysis with high orthogonality. For the root extract, as one of the analyzed samples, the optimization of the 1D and 2D gradients was carried out carefully. With this new modulator, much better peak separation and better peak shape were achieved compared to two-dimensional liquid chromatography system using a traditional standard (TS) modulator. With a similar approach, the other four parts of Buddleja davidii were well separated. Comparing the different analyzed parts, flowers and leaves showed the most complex profiles. MS and MS/MS data were obtained successfully, which demonstrated the potential of the proposed RPLCxHILIC-MS system in the constituents' analysis of herbal medicine. However, due to the lack of reported reference information, 24 compounds could be tentatively identified.