Abstract A simplified method with a dynamic Winkler model to study the seismic response of composite caisson–piles foundations (CCPF11 CCPF: composite caisson–piles foundation.) is developed. Firstly, with the dynamic Winkler model, the kinematic response of the CCPF subjected to vertically propagating seismic S-wave is analyzed by coupling the responses of caisson part and pile part. Secondly, a simplified model for the foundation–structure system is created with the structure simplified as a lumped mass connected to the foundation with an elastic column, and through the Fast Fourier Transformation (FFT) this model is enabled to solve transient seismic problems. Thirdly, the proposed method for the seismic response of CCPF-structure systems is verified by comparison against 3D dynamic finite element simulation, in which the Domain Reduction Method (DRM22 DRM: Domain Reduction Method.) is utilized. Lastly, the mechanism and significance of adding piles in improving the earthquake resistance of the foundation and structure is analyzed through an example with different soil conditions. Discovered in this study is that adding piles under the caisson is an efficient way to increase seismic resistant capability of the soil–foundation–structure system, and the main mechanism of that is the elimination of the pseudo-resonance.