Galactic cosmic rays (GCRs) are affected by solar modulation while they propagate through the heliosphere. The study of the time variation of GCR spectra observed at Earth can shed light on the underlying physical processes, specifically diffusion and particle drifts. Recently, the AMS-02 experiment measured with very high accuracy the time variation of the cosmic ray proton and helium flux between May 2011 and May 2017 in the rigidity range from 1 to 60 GV. In this work, a comprehensive three-dimensional (3D) steady-state numerical model is used to solve Parker's transport equation and is used to reproduce the monthly proton fluxes observed by AMS-02. We find that the rigidity slope of the perpendicular mean free path above 4 GV remains constant, while below 4 GV it increases during solar maximum. Assuming the same mean free paths for helium and protons, the models are able to reproduce the time behavior of the p/He ratio observed by AMS-02. The dependence of the diffusion tensor on the particle mass-to-charge ratio, A/Z, is found to be the main cause of the time dependence of p/He below 3 GV.