In the construction of underground rock engineering, complex geological conditions are commonly encountered, especially special conditions such as karst caves and faults, which bring great challenges to pile foundation construction. To study the accuracy of pile foundation drilling data under complex karst geology, this paper takes the pile foundation project in Yinshawan Karst Area, Jiujiang, Jiangxi as the engineering background, and summarizes the spatial characteristics of cave gradient angles based on the drilling data of the whole site, and uses the JC method to analyze the reliability of drilling data. The results show that the cave occurrence rate of the boreholes in this karst pile foundation construction site exceeds 50%, and the karst is extremely developed. According to the four spatial distribution modes of cave gradient angle, the drilling data with higher accuracy of karst cave information are preferentially selected. The JC method is used to analyze the reliability of the data with lower accuracy, and it is found that the gradient angles calculated by taking small, medium and large cave depths as reference values all follow a normal distribution, and the accuracy of identifying cave characteristics via boreholes increases significantly with the increase of cave depth. Finally, to control the supplementary drilling rate, a data screening and optimization strategy is proposed. Through the comparison of quantitative indicators, it is verified that controlling the supplementary drilling rate at about 5% can significantly improve the reliability of drilling results.