The invention provides an ecological sewage treatment system and method. The ecological sewage treatment system comprises a pre-treatment system, a biochemical treatment tank and an aftertreatment tank; a grille area and a sand setting area are sequentially arranged in the pre-treatment system, a sludge area and a microbiological treatment area are arranged upwards from the bottom of the biochemical treatment tank in sequence, a comprehensive treatment device is arranged in the microbiological treatment area, a water inlet pipe is arranged between the sludge area and the microbiological treatment area, and the aftertreatment tank is arranged at the downstream part of the biochemical treatment tank. According to the ecological sewage treatment system, the pre-treatment system, the biochemical treatment tank and the aftertreatment tank are arranged, and the comprehensive treatment device is arranged in the biochemical treatment tank, so that pollutants such as COD, ammonia nitrogen, total nitrogen and the like in the sewage can be effectively removed. The sludge area and the anaerobic area are arranged at the bottom of the biochemical treatment tank, and therefore, the overall biochemical treatment area can be ensured to be free of peculiar smell and secondary pollution to the environment is reduced.