The Central Asian Orogenic Belt (CAOB) is one of the world's largest and oldest accretionary orogens. The Junggar Terrane, located in the southwestern CAOB, is considered a key tectonic element to understand the evolution of the whole CAOB. However, given the lack of xenoliths and limited geophysical data with sensitivities to mantle depths, the nature of its basement and its deep lithospheric structure are still highly debated. Here we use a probabilistic inverse method to jointly invert newly processed Rayleigh wave dispersion data, surface heat flow, geoid anomalies, and absolute elevation. The output is a 3-D model of the seismic, temperature, bulk density, and compositional structure of the whole lithosphere beneath the western part of the Junggar Terrane. Our results reveal a subduction-shaped mantle anomaly beneath the western flank of the Junggar Basin that resembles closely the structure of a fossil subduction zone. We also confirm the presence of a thick lower crust beneath the basin with properties similar to those of basaltic rocks. On account of these results, we further conduct a hypothesis test and demonstrate that an “oceanic model” for the origin of the basement of the Junggar Basin explains the available geophysical and geochemical information better than other alternative models. Based on all these observations, we propose an evolutionary model for the western Junggar Terrane that reconciles a number of previously conflicting interpretations.