Compressive stress generated at collision fronts can propagate over long distances, inducing deformation within the continent's interior. Nevertheless, the factors governing the partitioning of intracontinental deformation remain enigmatic. The Altai Mountains serve as a type‐example of ongoing intracontinental deformation. Here, we investigate the crustal architecture of the Chinese Altai Mountains, using receiver functions obtained from newly deployed dense seismic nodal arrays. The new seismic results reveal distinct crustal features, including (a) a negative polarity discontinuity beneath Chinese Altai Mountains, suggesting a low‐velocity layer; (b) a north‐dipping mid‐crustal structure beneath the suture zone between East Junggar and Chinese Altai, indicating underthrusting of East Junggar's lower crust beneath the Chinese Altai Mountains; (c) a double Moho structure beneath East Junggar, revealing a high‐velocity lower crustal layer. In conjunction with constraints from previous multi‐disciplinary regional studies, the double Moho structures are interpreted as mafic restite from Late Paleozoic magma underplating. The addition of mafic materials can significantly enhance the rheological strength of East Junggar's crust, causing it to function as an indenter that thrust beneath the Chinese Altai Mountains during the subsequent convergence process. As a consequence, significant deformation occurs in the Chinese Altai region, resulting in the emergence of decollements, as evident by the negative polarity discontinuity. The presence of pre‐existing decollements makes the Altai Mountains region more susceptible to deformation, thereby facilitating the concentration of intracontinental deformation. These findings illuminate the evolution history of the Chinese Altai Mountains and highlight the great impacts of ancient tectonics on intracontinental deformation partitioning.