Ozone micro-bubble cleaning system was designed, and made to develop a unique technique to clean wafers by using ozone micro-bubbles. The ozone micro-bubble cleaning system consisted of loading, cleaning, rinsing, drying and un-loading zones, respectively. In case of the cleaning the silicon wafers of a solar cell, more than 99 % of cleaning efficiency was obtained by dipping the wafers at 10 ppm of ozone for 10 minutes. Both of long cleaning time and high ozone concentration in the wet-solution with ozone micro-bubbles reduced cleaning efficiency because of the re-sorption of debris. The cleaning technique by ozone micro-bubbles can be also applied to various wafers for an ingot and LED as an eco-friendly method.