Ubiquitylation is involved in most part of cellular processes, including protein degradation, autophagy, DNA damage repair, cell cycle, signaling transduction, gene expression, transcription regulation, inflammation and immune response. Instead of the formation of ubiquitylation, deubiquitinating enzymes (DUBs) hydrolyze monoubiquitylation and polyubiquitylation of substrates in response to ubiquitin-mediated pathways. There exits approximately 90 DUBs in human genome which regulate the enzymatic activity and recognition of substrates to control with precision the multi-layer complex cellular ubiquitin network. DUBs play diverse roles in cellular process, their dysfunctions direct to many serious diseases (like cancers, neurodegenerative disorders and infection diseases). Therefore, DUBs represent novel candidates for target-directed drug development. However, many physiologic functions of DUBs are still unknown. Whether they recognize different polyubiquitin chains and how to response signaling transduction accurately are unlear. In this review, we systematically surveyed the selectivity of the DUBs that we have known in hydrolyzing different ubiquitin chains and their mechanisms.