In this study, an integrative analysis of the gill-specific proteome at 0 h, 12 h and 36 h after alkalinity stress was performed to identify important regulators and pathways involved in alkalinity adaption of Exopalaemon carinicauda. This study reveals the first time-course, gill-specific, combined proteomic profiling associated with alkalinity adaption of E. carinicauda and provides new insights into the mechanisms underlying the molecular response to alkalinity stress in shrimp.