Analysis of a suspension of microorganisms is important in environmental and biomedical engineering. Previous studies had problems of high computational load in simulating many-body interaction of non-spherical swimmers. In this study, we propose a boundary element method (BEM), based on the double-layer representation, for calculating interactions of two squirmers in Stokes flow regime. By comparing the trajectories of squirmers calculated by both single- and double-layer representations, we show the accuracy of the method. The developed method has potential to deal with many-body interactions of non-spherical microorganisms.