In this study, we present whole-rock geochemistry and Sm-Nd data; zircon trace element, U-Pb, and Lu-Hf data; titanite U-Pb dating; and structural analysis of igneous and metasedimentary rocks of the Sawtooth metamorphic complex that provide insight into regional metamorphism, partial melting, and crustal thickening in the Idaho batholith segment of the Cordilleran orogen. Four magmatic events are revealed: (1) pre-tectonic felsic magmatism at ca. 156 Ma, (2) syn-tectonic mafic and felsic magmatism between ca. 100 Ma and ca. 92 Ma, (3) felsic magmatism concurrent with late-stage deformation at ca. 89–84 Ma, and (4) post-tectonic felsic magmatism at ca. 77 Ma. The multiple generations of felsic magmatism include a variety of sedimentary- and igneous-derived granitoids distinguished by zircon trace element compositions (e.g., U/Ce versus Th and Ce/Sm versus Yb/Gd) and were sourced from progressively more evolved crustal components as shown by Lu-Hf and Sm-Nd isotopic data. U-Pb data of metamorphic zircons and titanites from high-grade metasedimentary rocks suggest that regional metamorphism occurred from ca. 100–93 Ma, which was characterized by granulite-facies partial melting and concurrent growth of metamorphic zircons and garnets. The episodic magmatism in the Sawtooth metamorphic complex records pervasive melt migration in a hot, mid-crustal setting at ca. 100–92 Ma and additional magma ascent in a cool, upper-crustal setting at ca. 77 Ma. The uplift of the Sawtooth metamorphic complex from mid- to upper-crust was likely caused by underthrusting at lower crustal levels coupled with erosion and thinning of the upper crust. This work suggests that the crust of the Cordilleran hinterland in the Idaho batholith region underwent significant thickening from ca. 100–84 Ma, and a crust of Andean-like thickness was probably achieved by ca. 84 Ma. By ca. 77 Ma, the central Idaho crust started to thin likely due to mid-crustal flow and surface erosion. The new data from the Sawtooth metamorphic complex are consistent with the two major magmatic flare-ups in the Late Jurassic and Late Cretaceous in the U.S. Cordilleran orogen.