The invention discloses an organic matter pollutant treatment system. The system comprises a first base and a second base which are arranged on the two banks of a river. The river is transversely intercepted between the first base and the second base through a first cut-off wall, a second cut-off wall and a third cut-off wall, and a flocculation basin, a stirring basin and a sedimentation basin are sequentially formed. A wall body of the first cut-off wall, a wall body of the second cut-off wall and a wall body of the third cut-off wall are provided with water passing holes for the river to flow correspondingly. The flocculation basin, the stirring basin and the sedimentation basin communicate mutually. A flocculation mechanism, a stirring mechanism and a mud scraping mechanism are arranged in the flocculation basin, the stirring basin and the sedimentation basin correspondingly. The first base and the second base are provided with mud discharging basins correspondingly. Flocculation basins are arranged in the first base and the second base, and flocculating agents are stored in the flocculation basins and are conveyed into the flocculation mechanism through a water pump. The system can carry out flocculation, purification and degradation on organic pollutants in the river, the organic pollutants in the river can be treated, and the water environment is protected.