Abstract Chitosan-based nanocomposites have been studied in various fields, which urgently requires a more facile and efficient technique to fabricate nanoparticles with customized structures. In this study, Ag@methacrylamide chitosan/poly(ethylene glycol) diacrylate (Ag@MP) micropatterns are successfully fabricated by femtosecond laser maskless optical projection lithography (Fs-MOPL) for the first time. The formation mechanism of core-shell nanomaterial is demonstrated by the local surface plasmon resonances and the nucleation and growth theory. Amino and hydroxyl groups greatly affect the number of Ag@MP nanocomposites, which is further verified by replacing MCS with methacrylated bovine serum albumin (BSA) and hyaluronic acid methacryloyl, respectively. Besides, the performance of the surface-enhanced Raman scattering (SERS), cytotoxicity, cell proliferation and antibacterial were investigated on Ag@MP micropatterns. Therefore, the proposed protocol to prepare hydrogel core-shell micropattern by home-built Fs-MOPL technique is prospective for the potential applications in the biomedical and biotechnological fields, such as biosensors, cell imaging and antimicrobial.