Chitosan is a polymer with good biocompatibility, unique pH-responsive solubility, convenient modification and easier film-formability. Chitosan could serve as an active mediator between biological components and microfabricated devices to prepare biological micro electro mechanical systems (BioMEMS) with high selectivity and sensitivity. Recently, there has been a growing interest in BioMEMS based on biofabrication of chitosan. We reviewed the mechanisms and processes of three biofabrication methods based on chitosan, including directed assembly, enzymatic assembly and self-assembly. Current applications and research progress in biological, medical and environmental fields are also discussed. Finally, future research directions are prospected.