High industrial natural flow has been produced from the ultra-deep Cretaceous Bashijiqike sandstones (>6000 m) in the Qiulitage Structural Belt in the Kuqa Depression, Tarim Basin, northwestern China. However, the Cretaceous Bashijiqike reservoirs exhibit strong heterogeneity and significant reservoir quality variations. The complex in-situ stress state plays a critical role in reservoir quality; however, little research has been performed on the relationship between in-situ stress and reservoir quality, which constrains efficient hydrocarbon exploration and development. In order to clarify the in-situ stress-controlled reservoir quality variations, cores, thin sections and well log data are integrated to clarify the depositional microfacies, diagenesis and in-situ stress. The in-situ stress orientation and magnitude characteristics are investigated, and the distribution patterns of stress state are analyzed considering sedimentary environments and diagenesis. The results show that in-situ stress in Zhongqiu 1 gas field of Qiulitage Structural Belt remains unreleased since rare fractures are formed, and horizontal stress differences are greatly varied due to structural patterns, lithology assemblages and variations of geomechanical properties. The current maximum principal stress (Shmax) orientation is NW–SE, derived by image logs in the Cretaceous Bashijiqike reservoirs of Zhongqiu 1 gas field. Vertical stress (Sv) is determined by integrating bulk density of the overburden rocks, while the maximum horizontal principal stress (Shmax) and the minimum horizontal principal stress (Shmin) are calculated by the combined spring model using density and sonic logs. A significant negative correlation relationship is observed between measured porosity and horizontal in-situ stress differences (Δσ = Shmax − Shmin). The measured helium porosity is reduced to 9.4% when the Δσ is higher than 40 MPa. Intensive stress compression will contribute to a high compactional porosity loss (COPL), and COPL reaches 34.2% when the Δσ becomes higher than 40 MPa. Layers with lower Δσ values exhibit higher reservoir porosity and also higher natural gas production. Overall, favorable reservoirs are distributed at the center of sandbody in underwater distributary channel microfacies, and the sandstones are fine- to medium-grained and well-sorted with low in-situ stress differences. In-situ stress will control the compaction behaviors and the matrix porosity of sandstones, and also determines the hydrocarbon productivity. The results will provide insights into the reservoir quality variations in ultra-deep sandstones, and have implications for deep buried rocks with complex stress conditions worldwide.