Composite pile foundation has been widely used in ground engineering. This composite pile foundation system has complex pile-soil interactions under seismic loading. The calculation of vertical bearing capacity of composite pile foundation is still an unsolved problem if the soil around piles is partially or completely liquefied under seismic loading. We have completed indoor shaking table model tests to measure the vertical bearing capacity in a liquefiable soil foundation under seismic loading. This paper will use a numerical approach to analyze the change of this vertical bearing capacity under seismic loading. Firstly, the Goodman contact element is improved to include the Rayleigh damping. Such an improvement can well describe the reflection and absorption of seismic waves at the interface of soil and piles. Secondly, the Biot's dynamic consolidation theory incorporated an elastoplastic model is applied to simulate the soil deformation and the generation and accumulation of pore water pressure under seismic loading. Thirdly, after verification with our indoor shaking table test data, this approach is used to investigate the effects of pile spacing on liquefaction resistance of the composite pile foundation in liquefiable soil. The time histories of pore water pressure ratio (PPR') are calculated for the liquefiable soil and the vertical bearing capacity in partially liquefied soil is calculated and compared with our indoor shaking table test data at the 3D, 3.5D, 4D, 5D and 6D cases (D is the pile diameter). It is found that the pile spacing has some influence on the extent of soil liquefaction between piles. The vertical bearing capacity varies with liquefaction extent of inter-pile soil. The optimization of pile spacing varies with liquefaction extent. These results may provide some reference for the design of composite pile foundation under seismic loading.