The invention relates to a microorganism pollution control generation system, a preparation method of a microorganism pollution control fungicide and a microorganism pollution control method of the microorganism pollution control generation system. Pollution control generators are arranged in a controlled water area according to the design requirements, the pollution control generators in the controlled water area are arrayed in a staggered manner, water flow penetrates through the pollution control generators, each pollution control generator consists of a generator main support frame, an anchoring device, solar panels, a driving motor, a water paddle, a support frame, a fungi stick, a positioning rod and a floating appliance, the whole generator main support frame of each pollution control generator is a box-shaped frame; and each fungi stick is arranged on the corresponding positioning rod. The microorganism pollution control generation system is reasonable in design, simple in structure, obvious in effect, convenient to mount and low in cost, is energy-saving, can be reused, is high in cost recycling speed, and adapts to various different water areas; water circulating and physical and biological treatment technologies are combined; a water body environment of a polluted water area is improved effectively; organic substance degradation, water body environment control and improving effect are further improved; and therefore, the microorganism pollution control generation system can be widely popularized and used.