The Kuqa fold-and-thrust belt exhibits apparent structural variation in the western and eastern zone. Two salt layer act as effective decollements and influence the varied deformation. In this study, detailed seismic interpretations and analog modeling are presented to construct the suprasalt and subsalt structures in the transfer zone of the middle Kuqa and investigate the influence of the two salt layers. The results reveal that the relationship of the two salt layers changes from separated to connected, and then overlapped toward the foreland in the transfer zone. Different structural models are formed in the suprasalt and subsalt units due to the interaction of the two salt layers. The imbricate thrust faults form two broom-like fault systems in the subsalt units. The suprasalt units develop detached folds terminating toward the east in the region near the orogenic belt. Whereas, two offset anticlines with different trends develop at the frontal edge of the lower salt layer and the trailing edge of the upper salt layer, respectively. According to exploration results in this region, the relationship between suprasalt and subsalt structures has an influence on hydrocarbon accumulation. We believe that the connected deformation contains high-risk plays while the decoupled deformation contains well-preserved plays.