The invention discloses a method and irrigation system suitable for ecological governance of cliff fracture surfaces in karst stony mountain areas. The method includes the steps of 1, manufacturing plant growing grooves, preparing pulling anchors, setting the installation positions according to the palisades tendency, placing the grooves in a staggered mode, and after grooves are formed in palisades and anchoring plates are installed on the palisades, constructing and fixing the plant growing grooves, wherein each plant growing groove comprises a water groove and a soil medium groove which areseparated from each other; 2, sequentially filling the plant growing grooves with supporting granules, separation nets and soil mediums blended with soil, fertilizer, water-retaining agents and seeds; 3, building an irrigation facility on the top of a cliff, and carrying out irrigation with the cooperation of the plant growing grooves. The whole devices involve a main irrigation water pipe, the pulling anchors, rock hillslopes, drainage water pipes, the anchoring plates, plants, outer walls, water groove baffles, a soil layer, the separation nets, the soil medium grooves, a water supply layer, the supporting granules, the water grooves, clapboards, segments of the main irrigation water pipe, the plant growing grooves and a water collecting gutter. According to the method and irrigation system suitable for the ecological governance of the cliff fracture surfaces in the karst stony mountain areas, the problem that ecological governance is difficult to achieve on fracture surfaces of stony mountains with high gradient is solved, the vegetation recovery effect can be achieved fast, management and maintenance are simple and economical, and the governance effect can be maintained for along time.