The invention discloses a micro-flowing-water ecological breeding method for rare fishes in a rice field. The breeding method comprises the following steps of (1) selection of the rice field; (2) rice field transformation, wherein an enclosing ridge is built around the rice field, a water inlet and a water outlet are formed in the enclosing ridge of the two opposite corners of the rice field, then, fish ditches of cross-shaped structures are dug in the rice field, and finally, a feeding breeding ditch communicated with the fish ditches is dug in one side of the rice field; (3) rice planting, wherein manual transplanting of rice seedlings is conducted in rice planting areas in the rice field; (4) fry release, wherein 15 days after transplanting of the rice seedlings, fry are stocked in the feeding breeding ditch, and most of fry of sinocyclocheilus graham, schizothorax taliensis, neolissochilus benasi and spinibarbus sinensis bleeker are stocked; (5) feeding management, wherein after the planted rice seedlings turn green, artificial feed needs to be added into the feeding breeding ditch every day; (6) daily management. The allocation of mixedly-bred fry types is reasonable, planning for the rice field is proper, a scientific feeding mode is adopted, the growth speed of the fry is increased, and the yield of rice is also increased, so that the benefit of mixed fish breeding in the rice field is significantly increased.