The shrinkage microporosity formed during the directional solidification of Ni-based single crystal superalloys can significantly reduce the fatigue life of turbine blades, which may lead to a catastrophic flight accident due to the failure of aeroengines. We developed an integrated mesoscale model, which combined the shrinkage pressure drop from dendritic growth using cellular automaton method and X-ray microtomography characterization for Ni-based single crystal superalloys. The critical shrinkage pressure drop was derived from the simulation and compared to the empirical functions and experimental measurements. It was found that the pressure drop was so critical for predicting the microporosity accurately, and its relationship with the pore size and fraction was established via direct comparison to X-ray tomography. Using this integrated model, the pore size, percentage, and distribution as a function of directional solidification conditions can be successfully simulated. The model can predict small pores at the roots of the secondary dendrite arms in the early stage of solidification, and the large ones in the interdendritic liquid at the late stage of solidification. Therefore, this proposed approach has demonstrated to predict not only the influence of the processing conditions such as withdrawal rate on pore volume fraction, but also the root cause of pore size distributions.