Background: Erigeron multiradiatus (EM), a well-known traditional Tibetan medicine, has been used for hundreds of years to treat various chronic metabolic diseases. However, previous studies on EM have primarily focused on its pharmacognosy, identification, and clinical efficacy, which lacks a systematic material basis research to identify therapeutic targets. Objectives: In this study, we investigated the potential quality marker (Q-marker) and the pharmacological mechanisms of EM during treatment of diabetic microangiopathy (DM) using both ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS/MS) and network pharmacology. Materials and Methods: The chemical profile of EM was qualitatively identified for the first time by using UHPLC-QTOF-MS/MS. A network pharmacology methodology was then used to predict the major active components and key pharmacological pathways of EM in the treatment of DM. The compound-target network was constructed using Cytoscape software. Finally, virtual screening was conducted using molecular docking, and a cytopathological model was established by culturing vascular endothelial cells under in vitro conditions to verify the predicted bioactive markers. Results: A total of 26 compounds were identified and tentatively characterized in the chemical profile of EM based on the reference standards and mass spectral data. Network analysis was performed on 107 overlapping gene symbols, and seven bioactive constituents (e.g., quercetin, apigenin, luteolin, scutellarin, rutin, chlorogenic acid, and chrysoeriol) were identified as potentially bioactive markers. The results of molecular docking showed that quercetin, scutellarin, and rutin exhibited higher binding affinity to core targets than that of the remaining four compounds. The effects of quercetin, scutellarin, and rutin on vascular endothelial cells were investigated under in vitro conditions. According to the results, scutellarin and quercetin significantly inhibited the proliferation of vascular endothelial cells and decreased the levels of nitrous oxide, and reduced glutathione. Conclusion: This study showed that scutellarin and quercetin can be the Q-markers of EM due to their possible therapeutic efficacy in treating DM. It provided fundamental insight into chemical profiling, pharmacological mechanisms, and quality control of EM.