Transport properties of the MgB 2 thin films on Si, MgO and ZnO substrates with Ti buffer layer prepared by molecular beam epitaxy were investigated to clarify effects of the substrates and the Ti buffer layer on flux pinning. The critical current density J c of each sample shows different dependence on magnetic fields parallel to c-axis. However, the scaling analysis of the macroscopic pinning force for all the measured samples implies that the grain boundaries work as the dominant pinning centers for B//c. The pinning parameter for MgB 2 /Ti/Si estimated from the electric field E vs. the current density J characteristics shows the highest value among all the measured samples. This result is attributed to the high density of grain boundaries caused by the effect of both the Ti buffer and Si substrate in the growth process. Therefore, the selection of substrates and buffer layer strongly affects the flux pining properties of MgB 2 thin films and plays an important role in the determination of performance for superconducting devices and wires.