The carbonate-rich magmatic rocks of West Junggar are distributed in the Baijiantan and Darbut ophiolitic mélanges in the forms of extrusive rocks overlying the mélanges and dykes, either along the margins of the mélange or cross-cutting components of mélanges. Chilled margin and flow structures are present. A SHRIMP zircon U-Pb age of 39.7 ± 1.3 Ma indicates that these carbonate-rich rocks in West Junggar were formed during the Eocene. They have low concentrations in REEs, Th, U, Nb, Ta and are characterized by extremely low εNd(t), high (87Sr/86Sr)i ratios, relatively high δ18OV-SMOW values and high δ13CV-PDB values, which is similar with most sedimentary carbonates. Furthermore, no contemporaneous mantle-derived silicate rocks have yet been found in West Junggar. The carbonate-rich rocks in West Junggar are thus distinct from mantle-derived carbonatites and are interpreted to result from melting of the Carboniferous sedimentary carbonates at crustal levels, these rocks therefore being referred to as ‘crustal carbonatites’. The Eocene crustal carbonatites in West Junggar and other Cenozoic magmatic rocks in North Xinjiang are generally situated along regional strike-slip faults or fault intersections. Therefore, we propose that the reactivation of the Darbut and Baijiantan crustal-scale strike-slip fault zones (ophiolitic mélanges), due to the far-field effects of the Indian-Eurasian collision, enables decompression melting of the underlying continental lithospheric mantle. These resulting melts ascended to the lower crust through the strike-slip faults, causing partial melting of the Carboniferous carbonaceous sediments. The crustal carbonatites in West Junggar provide a new piece of evidence for Cenozoic magmatism in North Xinjiang and are also significant for the investigation of tectono-magmatic relations in North Xinjiang and the Central Asian Orogenic Belt.