This study used network pharmacology, bioinformatics, molecular docking and molecular dynamics simulations to evaluate the pharmacological mechanism of Jinshui Liujun decoction in treating chronic bronchitis. The network pharmacology constructed and analysed the drug-disease targets network. Microarray data analysis revealed CTSD as a key therapeutic target gene. Molecular docking and molecular dynamics simulations results indicated CTSD, can bind with β-sitosterol, cerevisterol, stigmasterol effectively. This study identifies the mechanism of action and gene expression of the key therapeutic target CTSD of Jinshui Liujun decoction in the treatment of chronic bronchitis, and verifies its binding stability with the key active components, aiming to provide new targets and research directions for the clinical treatment of chronic bronchitis.