The settlement of pile foundations is systematically investigated to provide an effective reference and design method for engineers and researchers. The mean vertical additional stress coefficient is defined based on the Mindlin solution, and a new method is developed for calculating the settlement of pile foundations by layering simply the soil layers with different compression modulus. The settlements of soils beneath the pile head are divided into two parts, settlements off the centerline of pile and on the centerline of pile, each of which is also considered to be generated by tip resistance and shaft resistance of pile groups. Through the case of pile groups, it is found that the settlement calculated by the proposed method of mean vertical additional stress coefficient is consistent with the result of layer-wise summation method when the soil layer is infinitely subdivided. At the end, the settlement of raft foundations by means of the method presented in this investigation is verified with the measured value of the engineering project in virtue of the program and finite element model, in which the program is compiled to obtain the compressive stiffness required for the finite element model.