During on-load starting process of an aviation wound-field synchronous starter/generator system, accurate rotor position information is required. Mechanical position sensor is susceptible to interference, increasing volume and weight, so online rotor position estimation is more desirable. Harmonics of main exciter (ME) caused by rotating rectifier are analyzed, and the 5th harmonic is used creatively to estimate rotor position in this paper. In this method, by performing coordinate transformation on stator current of ME, rotor position increment is extracted and obtained through a low-pass filter. Meanwhile, taking advantage of the unidirectional conduction characteristics of rotating rectifier, a new idea to estimate initial rotor position is also proposed. In this approach, pulse signal is injected into the stator winding of main generator (MM) every fixed electrical angle, then the maximum and minimum current response correspond to that of MM's S and N pole respectively. Finally, combine initial rotor position and position increment, continuous rotor position of MM can be gained. The proposed methods avoid dependence on the saliency of MM, require no high-frequency signal injection and do not need secondary magnetic pole identification. Effectiveness and advantages of the proposed method are verified on the test.