An ecological biowater purification system includes at least one water purification tank, each water purification tank including a water inlet, a water outlet, a water purification device, a suction device, a first backflow device and a second backflow device. In particular, the water purification device includes, in order, a sedimentation pool, an anaerobic pool, an anoxic pool, a level-1 and a level-2 biological filter pool, which communicate with one another via baffle boards and communication holes. Each suction device includes a plurality of suction nozzles and suction pipes for discharging precipitates out of the respective water purification tanks. The first backflow device is used to make some water in the level-2 biological filter pool flow back to the sedimentation pool, and the second backflow device is used to make some water in the level-1 and level-2 biological filter pools flow back to the anaerobic pool.