This dataset contains raw and processed TMT-based quantitative proteomic data generated from gill tissues of grass carp (Ctenopharyngodon idella) subjected to chronic salinity stress. Fish were gradually acclimated from freshwater (0‰) to elevated salinities (7‰ and 14‰) under controlled conditions. After stable acclimation, gill tissues were collected, pooled, and proteins were extracted, reduced, alkylated, and digested with trypsin. Peptides were labeled using TMT reagents and analyzed by nano LC–MS/MS on an Orbitrap Fusion Lumos mass spectrometer operated in data-dependent acquisition mode. The resulting MS/MS data were processed using Proteome Discoverer for protein identification and quantification. This proteomic dataset supports an integrated multi-omics analysis of gill adaptive responses to long-term salinity stress in grass carp.