We have found experimentally an anomalous thermoelectric characteristic of an n-type Si nanowire micro thermoelectric generator (μTEG). The μTEG is fabricated on a silicon-on-insulator wafer by electron beam lithography and dry etching, and its surface is covered with a thermally grown silicon dioxide film. The observed thermoelectric current is opposite to what is expected from the Seebeck coefficient of n-type Si. The result is understandable by considering a potential barrier in the nanowire. Upon the application of the temperature gradient across the nanowire, the potential barrier impedes the diffusion of thermally activated majority carriers into the nanowire, and it rather stimulates the injection of thermally generated minority carriers. The most plausible origin of the potential barrier is negative charges trapped at the interface between the Si nanowire and the oxide film. We practically confirmed that the normal Seebeck coefficient of the n-type Si nanowire is recovered after the hydrogen forming gas annealing. This implies that the interface traps are diminished by the hydrogen termination of bonding defects. The present results show the importance of the surface inactivation treatment of μTEGs to suppress the potential barrier and unfavorable contribution of minority carriers.