Abstract: The geological body in ultra-deep formation has high-strength energy accompanied with high pressure, high temperature, and high concentrated stress, which is prone to deformation and instability, leading to the high risk of disaster and accident. Therefore, the study of special geological factors is of great significance in drilling engineering practice of ultra-deep formation. In Tarim Basin, geological factors of the full strata in the drilling process are systematically summarized, and especially the non-target series are finely studied as the target layer. The background and occurrence environment of various geological factors affecting the ultra-deep drilling engineering are analyzed. Furthermore, the internal interaction between drilling engineering and geological factors is revealed by “sedimentary construction, tectonic transformation and sedimentary-tectonism coupling”, and the research and description methods of special geological factors are discussed. The results show that: (1) Compared with the medium-shallow oil and gas reservoirs, 95% of the drilling footage in ultra-deep well is in the non-target series, in which the drilling process directly affects the exploration and development progress; (2) Different from the medium-shallow oil and gas reservoirs, the surface conditions, complex lithology, geological trajectory, formation fluid and extremely high temperature and pressure field in ultra-deep formations are great challenges for drilling operation; (3) The systematic and scientific analysis of the special geological factors in ultra-deep drilling engineering, comprehensive understanding on oil and gas reservoir and an appropriate evaluation on well control safety risk are conducive to risk prevention and well location placement; (4) The analysis on special geological factors of the full strata further supports to construct a bridge between geology and drilling engineering, and promotes the integration of geology and engineering from concept to practice.