Abstract: Near-fault ground motions exhibit long-period velocity pulses and large-amplitude vertical components, obviously increasing structural damage. This study investigates a seismic metamaterial composite foundation (SMCF) to achieve simultaneous isolation of both horizontal and vertical seismic motions. A fast multipole indirect boundary element method was employed to establish the three-dimensional scattering field of seismic waves in the SMCF. Based on the verification of computational accuracy, the seismic isolation performance of the SMCF under near-fault pulse-type ground motions was analyzed. The parameter sensitivity study was conducted. The results indicate that the average horizontal and vertical isolation rates of the SMCF range from 37% to 63% and 24% to 43%, respectively. The central region above the SMCF achieves a maximum horizontal isolation rate of 75%, whereas the edge regions have a minimum of only 13%, highlighting a significant spatial variation in isolation performance. The sensitivities of the geometric and material properties of the SMCF, and seismic motion parameters, range between 0.26 and 0.38. The SMCF should extend beyond the structural foundation and undergo optimization to ensure seismic isolation performance. This study provides a new seismic isolation idea for near-fault structures.