SUMMARY Considering there is hardly any concerted effort to analyze the pile‐raft foundations under complex loads (combined with vertical loads, horizontal loads and moments), an analysis method is proposed in this paper to estimate the responses of pile‐raft foundations which are subjected to vertical loads, horizontal loads and moments in layered soils based on solutions for stresses and displacements in layered elastic half space. Pile to pile, pile to soil surface, soil surface to pile and soil surface to soil surface interactions are key ingredients for calculating the responses of pile‐raft foundations accurately. Those interactions are fully taken into account to estimate the responses of pile‐raft foundations subject to vertical loads, horizontal loads and moments in layered soils. The constraints of the raft on vertical movements, horizontal movements and rotations of the piles as well as the constraints of the raft on vertical movements and horizontal movements of the soils are considered to reflect the coupled effect on the raft. The method is verified through comparisons with the published methods and FEM. Then, the method is adopted to investigate the influence of soil stratigraphy on pile responses. The study shows that it is necessary to consider the soil non‐homogeneity when estimating the responses of pile‐raft foundations in layered soils, especially when estimating the horizontal responses of pile‐raft foundations. The horizontal loads and the moments have a significant impact on vertical responses of piles in pile‐raft foundations, while vertical loads have little influence on horizontal responses of piles in pile‐raft foundations in the cases of small deformations. The proposed method can provide a simple and useful tool for engineering design. Copyright © 2013 John Wiley & Sons, Ltd.