To reduce the effect of estimation position angle error caused by mutual inductance on sensorless control of switched reluctance motor (SRM) in clear command channel mode, a SRM rotor position estimation method is presented. Using this method, the effect of mutual inductance can be eliminated without measuring mutual inductance. First, different working states are analysed. When working at single-phase excitation, mutual inductance can be ignored, inductance model method is used to estimate the position angle. When working at two-phase excitation situation, mutual inductance is non-zero, based on flux linkage-difference a new method is used to eliminate mutual inductance influence. Finally, the proposed method is verified by experiments. Experiment results show that compared with the mutual inductance ignored methods, the proposed method has higher estimation accuracy. This method can realise stable and reliable running of SRM sensorless control in wider speed range.