A Corotating Interaction Region (CIR) is formed when the fast solar wind catches up with the slow solar wind. It is known that the intensity of Galactic Cosmic Rays (GCRs) is modulated by CIRs with the GCR intensity suppressed inside the CIR. Previous numerical studies were mainly confined to GCR protons. For this study we utilize a hybrid GCR transport model which incorporates a Magnetohydrodynamic (MHD) simulated solar wind plasma background with a CIR structure. Additionally, adopting appropriate mass, charge and local interstellar spectra, the hybrid transport model is applied to GCR protons and the two helium isotopes. It is found that both proton and total helium studied at 0.3 GV are modulated by the CIR with their fluxes being depressed. However, the modulation for protons and helium is different with helio-longitude, and interestingly the ratio of the proton to helium flux varies with longitude. Similar results are found for the way in which the two helium isotopic fluxes vary.