The Pamir plateau lies at the western end of the Tethys domain recording the entire evolution from the opening of the Proto-Tethys to the final closure of the Neo-Tethys. During this long-term evolution, the details of the initial subduction of the Paleo-Tethys and the final amalgamation of the main terranes in the Pamir are still controversial. The Carboniferous bimodal volcanic sequences along the Northern Pamir may supply the key evidence to reveal the subduction process of the Paleo-Tethys Ocean. This study presents the detailed stratigraphic architecture, petrography, geochronological and geochemical data of the Carboniferous−Permian volcanic rocks along the Northern Pamir in western China bordering Tajikistan. Zircons from two plagioclase phenocryst-rich basalts, and an andesite, volcanic agglomerate, and granitic sill emplaced in the basalts yield concordant ages of 319.5 ± 2 Ma, 322.7 ± 1.6 Ma, 288.7 ± 2.5 Ma, 301.6 ± 4.2 Ma, and 300.4 ± 1.5 Ma, respectively. The basalts show mid-oceanic-ridge basalt−like geochemical features with flat to depleted light rare earth element trends [(La/Yb)N = 0.68−1.82], depleted whole-rock εNd(t) (6.44−7.85), and zircon εHf(t) (6.3−10.1) values, suggesting they are primitive magmas derived from a depleted mantle source metasomatized by earlier subduction in line with their low Nb/La ratios (0.30−0.64). As for the intermediate-acid volcanic rocks (andesite and dacite), they show enrichment of large ionic lithophile elements (e.g., Rb, Ba, and Sr) and depletion of high field strength elements (e.g., Nb, Ta, and Ti) as well as negative εNd(t) values ranging from −0.97 to −0.75, demonstrating that they are primitive magmas derived from partial melting of the metasomatized lithospheric mantle source, followed by crystal fraction of hornblende, plagioclase, and minor quartz. Taking together the stratigraphic features, rock associations, and geochemical signatures, the Carboniferous basalts share most features with the Okinawa and the Mariana back-arc basalts. Integrating the new data with the previous studies, we construct a detailed evolution process of the Paleo-Tethys Ocean at the Pamir, i.e., extension of the filled residual Proto-Tethys Ocean between the Tarim and the Northern Pamir induced by the northward Paleo-Tethys subduction in the early Carboniferous, gradually waning of the back-arc basin from the late Carboniferous to the Early Permian, and finally, the closure of the Paleo-Tethys Ocean led to the amalgamation of the Northern, the Central, and the Southern Pamir, resulting in the initial architecture of the Pamir.