This paper explores the influences of the pore size effect (represented by a nonlocal parameter) and the heterogeneous effect of the medium (represented by a size factor) on the dynamic response of saturated soil foundations. Based on the strain gradient nonlocal Biot theory, the calculation program for the dynamic response of a saturated soil foundation subjected to cyclic load was compiled using the meshless method. Therefore, the accuracy of the meshless method program was verified. Results indicate that the responses of displacement and pore pressure at observation points are delayed with the increase in nonlocal parameters, maintaining the scale factor as constant. By contrast, the responses are advanced with the increase in the scale factor, maintaining the nonlocal parameter as constant. This finding indicates that the macro-modulus of the system will be decreased considering the pore size effect, which will be increased considering the heterogeneous effect of soil structures. Methods and ideas for solving dynamic problems of saturated soil using the proposed meshless method in this paper could provide references for future research on similar problems.