The switching frequency of high-power medium-voltage electronic devices is usually kept low to restrain the switching losses. Owing to the low switching frequency, the harmonic current components of the stator were increased, which would also result in difficulties in balancing the neutral point potential. Extracting the fundamental content by low-pass filter produced a signal delay and amplitude attenuation, which could not meet system requirements of high performance control. In this paper, a novel hybrid fundamental stator current observer at different coordinates for the electrically excited synchronous motors was designed based on the observer theory and the complex matrix model. This kind of hybrid observer could extract the fundamental component of the stator current instantaneously, and obtain a relative nice robustness with the variation of the speeds and parameters mismatching. Taking the observed the stator current as the feedback signal, a balance have been obtained for the neutral point potential with a three-level inverter topology. The MATLAB simulation and digital signal processor experimental results verify the availability of the novel hybrid current observer.