Western Makran has a very heterogeneous and complex crust due to the structures related to subduction of Arabian plate, Sistan sedimentary basin, and the Jazmurian and Hamuni-Mashkel depressions. We used the ambient noise adjoint tomography method, a method with higher resolution than conventional tomography methods, to improve the crust and upper mantle shear velocity model. We were able to reduce total misfit by about 65% relative to the latest shear velocity model obtained by conventional method. The results show the existence of three deep sedimentary basins in the eastern corner of the Jazmurian depression (~15 km), Sistan sedimentary basin (~20 km) and the southern half of Makran accretionary wedge (~20 km). A high velocity region is detected within the accretionary prism which could be related to deep ophiolites.