A comprehensive three-dimensional numerical model for the modulation of cosmic rays in the heliosphere is applied to investigate the relative roles of the time dependence of the three diffusion coefficients on the p/He ratios at rigidities below 3 GV. At these rigidities the ratios have been observed by PAMELA and AMS to have a significant time variation. We find that the contribution of the time dependence of perpendicular diffusion in the radial direction of the heliosphere is the dominant cause of this observed time variation and not any fundamental difference between the solar modulation of galactic protons and helium.