The numerical prediction of effective diffusivity in hardened cement paste has been a hot point in the past few decades. However, the shape of cement powder is normally over-simplified as sphere in most models, which may influence the accuracy of prediction. To assess this effect of the shaped simplification on the prediction of effective diffusivity in cement paste, a microstructure-based model considering irregular-shaped cement powders that are close to the real one, and spherical cement powder respectively, is presented to simulate the hydrating cement pastes between aggregates (interfacial transition zone and bulk cement paste) and predict their effective diffusivities. The results indicate that the effect of the shape of cement powder on the distributions of capillary pore and unhydrated cement is weak. Furthermore, compared to the irregular-shaped cement powder, the diffusivity in cement paste simulated using spherical cement powders is overestimated by 0–40%. It is ascribed to three discrepancies, i.e., the shape of initial cement powder, the formation of capillary pore structure, and the morphology of C-S-H. However, the predicting error using spherical cement powder is still acceptable by contrast to the large difference of diffusivity in hardened cement paste with cement hydration, i.e., normally two orders of magnitude difference between early and later curing ages.