This dataset contains LC-MS/MS-based proteomic data generated from muscle/myoseptal tissues of wild-type, heterozygous runx2b mutant, and homozygous runx2b mutant Culter alburnus individuals. The study aimed to characterize proteomic changes associated with runx2b-mediated intermuscular bone reduction and loss. Three biological replicates were analyzed for each genotype group. Differential protein abundance analysis and integrated transcriptomic-proteomic analysis were used to identify candidate proteins and functional modules associated with extracellular matrix remodeling, cytoskeletal organization, calcium signaling, muscle contraction, and osteogenic regulation during intermuscular bone development.