Numerical simulations can provide valuable insights for the optimization of design and operational management; however, they are often impractical and computationally intensive. Machine learning methods are appealing to these problems due to their sufficient efficiency and accuracy. In this study, a novel framework for predicting the impact responses of foam-filled multi-layer lattice composite structures (FMLCSs) was proposed by combining the accurate finite element (FE) analyses, surrogate models, fast Fourier transform (FFT) method, and inverse FFT (IFFT) method. Firstly, reliable FM models were established to simulate the crashworthiness of the five FMLCSs under impact loading, including an analysis of energy transformation. Subsequently, surrogate models, namely radial basis function (RBF), polynomial response surface (PRS), Kriging (KRG), and back propagation neural network (BPNN), combined with methods of FFT and IFFT, were employed to predict the impact force-time series of the FMLCSs. More than 1000 frequency points were employed for each type of FMLCS, and all the R-square (R2) values of the established surrogate models exceeded 0.95, indicating that the proposed framework accurately predicted the impact duration and impact responses in the frequency domain. In addition, parameter sensitivity analysis revealed that a high peak impact force was accompanied by a short impact duration. Moreover, increasing the lattice-web height resulted in a significant increase in the impact duration.