Novel inflammatory bowel disease (IBD) therapeutic drugs, mainly biologics that neutralize pro-inflammatory factors and janus kinase inhibitors that inhibit cytokine-mediated signal transduction, face problems including low efficacy rates, limited therapeutic benefits, and infection risks. It is an important task to find proteins that broadly regulate a variety of cytokines and to develop corresponding drugs. Cathepsin C (CTSC) mediates neutrophil-related inflammatory, participates in the recruitment and activation of inflammatory cells, and regulates cytokines levels, and is considered an ideal target for IBD treatment. In this study, starting from the in-house molecule, through medicinal chemistry and target-based design, a novel CTSC inhibitor B22 with IBD therapeutic efficacy was discovered. In vitro target verification and mechanism study indicated that B22 inhibit CTSC activity by binding to S2 pocket and S1 site, further inhibiting downstream serine protease activity. In addition, B22 exhibited anti-inflammatory activity and regulated various cytokines levels. In vivo studies highlighted B22 bears acceptable toxicity and suitable pharmacokinetic properties, and displays anti-inflammatory activity in IBD model. In conclusion, B22 is a potential anti-inflammatory molecule for IBD by targeting CTSC and deserves further research.