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The Altyn Tagh Fault (ATF) has important controls on the sedimentation in the Qiadam basin. In this study, detailed sedimentological and geochemical analyses were presented to deduce the impact of the ATF on deposition in the Honggouzi area during the early-middle Miocene, which is a significant period for ATF strike-slip movements. The early-middle Miocene strata of the Honggouzi area are deposits of a fan delta and show retrogradation by sedimentary characteristic of drilled wells. The elementary geochemical analysis indicates that the early-middle Miocene deposits of the Honggouzi area was mainly composed of felsic rocks formed in the continental island arc or active continental margin setting and derived from a segment of the Altyn Tagh Mountains (ATM). In addition, the seismic data suggests that (1) the nearly NW-SE-directed anticlines, which were caused by the flexural deformation, and uplift of the piedmont area in the northwestern Qaidam Basin occurred simultaneously during the early-middle Miocene, and (2) retrogradational sedimentation was caused by greatly increased accommodation during the early-middle Miocene when the subsidence amount of flexural deformation was larger than the uplift amount. The flexural deformation, uplift of the piedmont area of the northwestern basin, and uplift of the ATM were all controlled by the ATF strike-slip movements and therefore were the ways in which the ATF strike-slip movements affected the early-middle Miocene deposition of the Honggouzi area.