Insulin resistance (IR) of skeletal muscle is critical for type 2 diabetes mellitus (T2DM). Herein, we tried to identify genes critical for the IR of skeletal muscle in T2DM based on the Gene Expression Omnibus (GEO) database and in vitro cell experiments. Data sets related to skeletal muscle samples of T2DM patients were downloaded from the GEO database, and clinical information on T2DM patients in the GSE18732 data set was extracted, followed by determination of the module most related to T2DM. Then, the key genes were found after intersection analysis, followed by the analysis of the diagnostic markers of IR of skeletal muscle in T2DM. Subsequently, the mechanistic role of the key gene was illustrated by in vitro experiments in palmitate-stimulated human skeletal muscle cells (SkMCs). The black module was most associated with T2DM. Following intersection analysis with differential genes, eight key genes were obtained, including CTSB, ESR2, OAT, MSTN, PVALB, MAPK6, PHKB, and ATP2B2. Among them, CTSB had the highest diagnostic value, and its expression adversely correlated to the homeostasis assessment model for IR. Furthermore, in vitro experiments indicated that overexpression of CTSB inhibited the protein degradation of IRS-1 and GLUT4, thus attenuating the IR in palmitate-induced human SkMCs. The current study demonstrated that CTSB could act as a diagnostic marker of skeletal muscle IR in T2DM, and its overexpression inhibited palmitate-induced IR in human skeletal muscle cells.