Here we report a rapid approach for qualitative analysis of iridoid glycosides and caffeoylquinic acids (CQAs) in Re Du Ning Injections using a Direct Analysis in Real Time (DART) ionization source coupled with quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS). In this approach, DART/MS and DART MS/MS analyses in both negative and positive ion modes were performed to characterize two iridoid glycosides and six CQAs in reference solutions and Re Du Ning Injections. Fragmentation pathways of two kinds of natural compounds were summarized. DART-MS tended to break down some labile bonds in di-CQAs. The di-CQAs yielded abundant fragment ions in the (−) mass scan spectra. Collision-induced dissociation techniques were used to fragment the precursor ions and the product ions. Moreover, differentiation of the isomers of CQAs was possible by using the relative peak abundance and characteristic ion species in MS/MS spectra. DART-MS was also employed to obtain a chemical fingerprint of Re Du Ning Injections for rapid qualitative analysis of this Chinese medicine preparation. DART/Q-TOF MS/MS has shown potential to be used as the real-time detection method for Re Du Ning Injections.