Natural fractures are important reservoir spaces and seepage channels for oil and gas. In complex structural deformation zones, fractures are obviously controlled by faults, but the laws and modes of fracture formation are not yet clear. This study investigates natural fractures developed in complex fault zones in the Kuqa depression. Based on geological observation, fracture interpretation from imaging logging, and theoretical analysis, a “fault-controlled fracture coefficient (K)” is defined and calculated to reveal the development and distribution pattern of fault-controlled fractures in the study area. The results indicate (1) the thrust faults obviously control both the occurrence and development of natural fractures, where the fracture density is exponentially inversely proportional to the distance from the fault, and the fault-controlled fracture zones can be divided into strongly-controlled, weakly-controlled, and regional fracture zones with increasing distance to the fault. (2) Among the strike-slip faults, high-angle oblique faults develop fault-controlled fracture zones where fracture development is significantly affected by the scale of the faults; while fractures associated with oblique thrust faults are mainly developed within the fault zone, and the width of the fault zone varies along the strike direction. (3) The fault-controlled fracture coefficient (K) is defined as the ratio of the width of the strongly-controlled fracture zone to the fault displacement (slip displacement). According to the analysis, the K values of thrust faults in the Kuqa depression ranged between 1.50-1.80, and that of strike-slip faults ranged between 0.125-0.150. The results have both theoretical and practical significance for guiding oil and gas exploration and development in complex structural deformation zones.