ZnO has shown great promise for application in optoelectronic devices, in which the modulation of conductivity is crucial to device performance. In this paper, we have applied the Monte Carlo method to analyze the mobility of single-crystalline and polycrystalline MgZnO/ZnO heterostructure thin film layers. The effects of grain boundary scattering and ionized impurity scattering, as well as phonon scattering, are considered. Our studies show that, with careful design of modulation doping that considers the effects of spontaneous and piezoelectric polarization, the grain boundary potential can be suppressed to improve the mobility of the ZnO layer by at least one order of magnitude. Simulation results are also confirmed by our experimental work, which shows that the polarization effect does play an important role in attracting carriers and increasing the mobility.