Background It is essential to identify the chemical components for the quality control methods establishment of Chinese Classical Formula (CCF). However, CCF are complex mixture of several herbal medicines with huge number of different compounds and they are not equal to the combination of chemical components from each herb due to particular formula ratio and preparation techniques. Therefore, it is time-consuming to identify compounds in a CCF by analyzing the LC-MS/MS data one by one, especially for unknown components. Methods An ultra-high pressure liquid chromatography-linear ion trap-orbitrap high resolution mass spectrometry (UHPLC-LTQ-Orbitrap-MS/MS) approach was developed to comprehensively profile and characterize multi-components in CCF with Erdong decoction composed of eight herbal medicines as an example. Then the MS data of Erdong decoction was analyzed by MS/MS-based molecular networking and these compounds with similar structures were connected to each other into a cluster in the network map. Then the unknown compounds connected to known compounds in a cluster of the network map were identified due to their similar structures. Results Based on the clusters of the molecular networking, 113 compounds were rapidly tentative identification from Erdong decoction for the first time in the negative mode, which including steroidal saponins, triterpenoid saponins, flavonoid O-glycosides and flavonoid C-glycosides. In addition, 10 alkaloids were tentatively identified in the positive mode from Nelumbinis folium by comparison with literatures. Conclusion MS/MS-based molecular networking technique is very useful for the rapid identification of components in CCF. In Erdong decoction, this method was very suitable for the identification of major steroidal saponins, triterpenoid saponins, and flavonoid C-glycosides.