The natural electric field frequency selection method has good effects on ground water exploration, but is short of theoretical research. The anomaly of a vertical fault of frequency selection method was studied from theory and practice. According to classical theory of magnetotelluric sounding, firstly, based on the Maxwell equations and the boundary conditions, the analytic expressions of horizontal electric field components on the ground was derived for a vertical fault in a harmonic magnetotelluric field. Secondly, all parameters of the model were supposed, and anomalous curves of horizontal electric field intensity on the ground main profile were obtained. At last, theoretical curves were compared with practical curves. Their curves had similar characteristics, and therefore the anomaly of frequency selection method was caused by natural induced electric field.