A multi-frequency megasonic system for nano-particle removal was developed. In design process, finite element analysis was performed and anti-resonance frequency for 1 MHz actuating, was predicted as 995 kHz with 0.5% error compared with the measured value of 1000 kHz. In addition, anti-resonance frequency of 2998 kHz was obtained for 3 MHz, which coincided with the measured value. For the verification of the system performance, acoustic pressures of the developed waveguide were measured and compared with a commercial megasonic system. The result revealed that the developed one can show relatively better distributions. To assess cleaning ability, particle removal efficiency (PRE) tests were processed and 56.1% PRE improvement was achieved compared with a conventional product. Considering these results, the developed system can be applied to nano-particle cleaning process with higher efficiency.