This paper presents an second harmonic elimination method based on the impedance variation scheme. Through the power quality analysis from the nonlinear loads connected on the power system, the second harmonic problems have been analyzed with a case study analysis and the experiments. In the paper, the second Harmonic generation was simulated with a single phase SCR rectifier and the analytical model is proposed for the second harmonic generation. A novel impedance variation scheme is proposed and analyzed to eliminate the second harmonic. The experiment has been performed on the 60(MVA) industry manufacturing plant. The experimental result demonstrates the proposed impedance variation scheme successfully operate on the 60(MVA) industry manufacturing plant.