The invention provides a method and a system for automatic cleaning of an underwater holder. The system comprises a land industrial control computer, a holder controller, and an underwater camera. The method comprises: the land industrial control computer clipping a real-time image transmitted by the underwater camera as a static image, performing image quality evaluation on the real-time static image and a clear reference image, to obtain a quality evaluation index, using the quality evaluation index as basis that whether a lens is polluted, when image quality is too low, determining that the lens is polluted and cannot take high-quality pictures and needs cleaning; the land industrial control computer sending a cleaning command to the holder controller through a 232 bus, and the holder controller driving a cleaning brush motor to clean the lens. Using the method of automatically identifying pollution degree of the lens and cleaning the lens effectively solves problems that the underwater holder is easy to pollute and manual cleaning is difficult. Compared with a method of driving a cleaning brush at regular time, the method cleans the lens when the lens is polluted, so as to effectively reduce energy consumption.