The invention relates to a comprehensive treatment method for wastewater generated in iron phosphate production, the wastewater is divided into washing water and mother liquor, the comprehensive treatment method is characterized by comprising the following steps: (S1) washing water treatment: (S2) mother liquor treatment: A, fluorine removal; b, phosphorus removal; c, removing manganese; d, producing by-product calcium sulfate; e, removing calcium and magnesium; f, removing ammonia; and G, circulating. Zero emission of the iron phosphate wastewater is realized through process optimization, and according to different properties of various impurities, grading separation and recovery are performed, so that the resources are recovered to the maximum extent. According to the method, fluorine ions in the wastewater are removed in the early stage, a high-quality iron phosphate byproduct can be obtained, manganese dioxide and calcium sulfate are obtained in the subsequent stage, new impurities are not introduced while resources are recycled, a little surplus is obtained through cost benefit accounting, and the method is a comprehensive wastewater treatment method with great economic value.