The invention relates to a self-purifying-type small circulating pool system for germ plasma resource protection, which is characterized in that the self-purifying-type small circulating pool system comprises an aquiculture water pool, a water guide pipe is arranged at the left rear part of the aquiculture water pool, the aquiculture water pool and a water isolating pool are communicated through the water guide pipe, floating plants are planted in the water isolating pool and a filter screen is arranged in the water guide pipe; a water isolating wall is arranged at the front of the water isolating pool, a group of ditches are arranged on the upper end surface of the water isolating wall, and the water isolating pool and an artificial underflow wetland pool at the front are communicated through the ditches; and an air-lift-type pipe is arranged at the front part of the artificial underflow wetland pool, the air-lift-type pipe consists of a perforated pipe, a water inlet pipe and an air stone, small holes are arranged in the side peripheral wall of the perforated pipe, the diameter of the small holes is smaller than the diameter of particles in the artificial underflow wetland pool, the side wall of the perforated pipe is connected with one end of the water inlet pipe, the artificial underflow wetland pool and the aquiculture water pool are communicated through the other end of the water inlet pipe, the air stone is arranged in the water inlet pipe and the air stone is connected with an external air pump. The water isolating pool, the artificial underflow wetland pool and the aquiculture water pool form an anticlockwise water circulating system.