INTRODUCTION: Wendan decoction (WDD), a classic Chinese medicine formula, has been used for the treatment of insomnia for hundreds of years. However, the current research on the chemical composition and the material basis of the medicinal effect of WDD is not perfect, which limits further research on it. OBJECTIVES: In the present study, we aimed to propose a methodology for the quality control of WDD based on qualitative and quantitative analysis of its components. METHODS: The chemical composition of WDD was identified through UPLC-Q-Exactive Orbitrap MS technology. Then, high-performance liquid chromatography was utilized to establish the fingerprint of 10 batches of WDD and determine the content of some common peaks. The quality evaluation and quality control of WDD were implemented from three aspects: chemical composition, fingerprint, and content determination. RESULTS: The study initially identified 113 chemical components, including 51 flavonoids, 13 amino acids, seven nucleotides, five alkaloids, eight phenylpropanoids, eight terpenoids, 12 organic acids, and nine other compounds. In this study, the fingerprint of WDD was established by HPLC, and a total of 23 common peaks were found and seven common peaks were determined. The similarity (R) between 10 batches of WDD fingerprints and reference fingerprints was greater than 0.993. The results of methodological verification met the requirements. CONCLUSION: Based on the three dimensions of qualitative analysis, fingerprint, and content determination, this study explored the quality control of WDD and selected seven flavonoids as quality evaluation indexes of WDD, thus laying a solid foundation for subsequent pharmacodynamic research.