In the construction of underground rock projects, complex geological conditions are often 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 basis, and proposes the spatial characteristics of cave gradient angle 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 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 cave information are preferentially screened out. The JC method is used to analyze the reliability of the data with lower accuracy, and it is found that the gradient angles calculated with small, medium and large cave depths as reference values all obey the normal distribution, and the accuracy of drilling hole identification of cave characteristics increases significantly with the increase of cave depth. Finally, on the basis of controlling the supplementary drilling rate, a data screening and optimization strategy is proposed. Through the comparison of quantitative indicators, it is verified that the supplementary drilling rate controlled at about 5% can significantly improve the reliability of drilling results