Relative to the power grid, the short-capacity system has smaller inertia and weaker ability to bear disturbance. As a result, the synchronous generator in short-capacity system will be greatly influenced by harmonic. To reveal how harmonic influence the generator, this article analyzed how harmonic current will influence the output voltage. Deduced a formula that can describe the electromagnetic torque pulsation brought by the theory of Instantaneous Power, which can explain why generator’s shaft vibrates. Then this article evaluated the applicability of current filtering methods in view of characteristics of the small capacity of the system. As a result, it was demonstrated that active filtering method is best suited for small capacity system. At last, it conducted the experiment that diesel generator set supply power to non-liner load to demonstrate the conclusion of theoretical analysis.