During the stability analysis of the deeply covered karst pile foundations，designers find it difficult to choose a suitable calculation method due to the large differences in the results of the different methods recommended by different specifications. Considering the deep cover characteristics of the karst in the site，this paper used the finite-element numerical simulation in Madis GTS to calculate the deformation of the karst cave roof and analyzed the impact of pile foundation loading on the karst cave roof. After a comparison with the theoretical calculation results，this paper proposed a parameter value standard for theoretical calculation formulas and a minimum safe thickness theory for deeply covered karst roofs. This paper provides an accurate and reliable basis for pile foundation design.