In this article, the megasonic cleaning system for cleaning micro/nano particles from flat panel display (FPD) surfaces was developed. A piezoelectric actuator and a waveguide were designed by finite element method (FEM) analysis. The calculated peak frequency value of the quartz waveguide was 1002 kHz, which agreed well with the measured value of 1003 kHz. The average acoustic pressure of the megasonic cleaning system was 43.1 kPa, which is three times greater than that of the conventional type of 13.9 kPa. Particle removal efficiency (PRE) tests were performed, and the cleaning efficiency of the developed system was proven to be 99%. The power consumption of the developed system was 64% lower than that of the commercial system. These results show that the developed megasonic cleaning system can be an effective solution in particle removing from FPD substrate with higher energy efficiency and lower chemical and ultra pure water (UPW) consumption.