This article presents the performance comparison of Series Active Power Filter (Series APF) based on seven and nine multi-level Neutral Point Clamped (NPC) inverters using the same control scheme. The Series APF is one of the most efficient and effective modern custom power devices used in power distribution networks to compensate voltage harmonic and all voltage disturbances. The conventional configuration based on voltage source inverter (VSI) operated at very high switching frequency presents several drawbacks and limited for low power applications. To overcome these problems and improve the output voltage different multi-level are used in various power application in particular Flying Capacitor (FC), Cascade H-Bridge (CHB) and multi-level (NPC) inverters. In this study seven and nine-level (NPC) inverters are proposed for active power filtering system; these inverters present diverse advantages include the capability to reduce the harmonic content, decrease the voltage or current ratings of the semiconductors and mainly they can work at low switching frequency. To generate switching pulses Multi-Carrier Level-Shifted Pulse Width Modulation (MC-LSPWM) control technique is adopted with modified P-Q control strategies. To verify the accuracy and the performance of the proposed Series APF models, simulation is performed using MATLAB-Simulink platform and SimPowerSystem Toolbox. The obtained results show the superiority of series APF based on nine-level in term of THDv reduction compared to the systems with seven-level inverter topology.