Background: Mori Folium, Mori Ramulus, Mori Fructus, and Mori Cortex are traditional Chinese medicines derived from distinct organs of mulberry (Morus alba L.). Intriguingly, their efficacies are different. Objectives: In this study, we aimed to systematically analyze the similarities and differences in the chemical composition of the aforementioned four medicines and to explore their bioactive components of anti-inflammatory and antitussive activity. Materials and Methods: High-performance liquid chromatography with electrospray ionization mass spectrometry (HPLC-ESI-MSn) was used to identify the various compounds present in each of the four medicines from the methanolic extracts and different polar fractions of aqueous extracts. Moreover, the identified compounds were docked against anti-inflammatory or antitussive targets by means of the molecular docking tool, molecular operating environment 2018. Results: A total of 77 compounds were identified from the four study materials, of which 30 were identified in Mori Folium, 27 compounds in Mori Ramulus, 23 compounds in Mori Fructus, and 46 compounds in Mori Cortex, and they had 14, 4, 3, and 26 compounds that were specific to them, respectively. The results of molecular docking indicated that quercetin, chlorogenic acid, and isoquercitrin, the shared compounds of the four medicines showed strong anti-inflammatory activity. Of note, the top 10% of compounds with better anti-inflammatory activity were mostly identified in Mori Cortex, whereas the least in Mori Fructus. Moreover, out of the top 10% of compounds with better antitussive activity, 11 compounds were identified in Mori Cortex, and only 2 or 3 compounds were identified in the other three medicines. Conclusion: The results of this study are consistent with the clinical application of the four study medicines derived from mulberry, which further supports the fact that their efficacy is dependent on their chemical composition.