In order to enhance the efficiency of construction in hydraulic and hydropower projects, the use of ultra long, high angle inclined shafts have become increasingly common. However, severe deviations in the pilot hole drilling significantly affect the tunneling accuracy of the inclined shaft. Therefore, the factors influencing the deviation of the pilot hole in the shaft with a length 277 m, and an inclined angle 60° are analyzed in this paper, and a model for calculating the drilling trajectory of the pilot hole is established. The average-angle method is employed to calculate the drilling path, and further, a correction technique for ultra-long, high-angle inclined shafts is proposed, which involves zoning strategies and sectional adjustments tailored to specific conditions. The research findings indicate that geological factors such as rock anisotropy, interbedded soft and hard strata, and fault or fracture zones, as well as technical factors including drill tool structure, drilling methods, and the weight of the drill bit, are all responsible for deviations in the drilling trajectory. These factors lead to significant misalignment in the pilot hole, which in turn affects the accuracy of the inclined shaft. Field application of this approach in a particular project showed that the accuracy of the final inclined shaft breakthrough reached 0.18%. The results of this study offer valuable insights and practical guidance for drilling inclined shafts under similar geological conditions, and can assist in improving the precision and efficiency of such operations in the future.