The invention discloses a treatment system and a treatment process for wastewater containing fluorine and phosphorus, and belongs to the technical field of industrial wastewater treatment. The treatment system comprises a pretreatment unit, a primary treatment unit, a secondary treatment unit, a discharge tank and a sludge reduction unit. According to the treatment system and the treatment processprovided by the invention, ultra-clean discharge of wastewater containing fluorine and phosphorus can be realized, and after the wastewater is subjected to deep fluorine and phosphorus removal treatment, at least the fluorine content in the wastewater can be reduced to 1.0 mg / L or below, the total phosphorus content in the wastewater can be reduced to 2.0 mg / L or below, and for some special areas, the total phosphorus content can be further reduced to 0.5 mg / L or below; the system and the process are suitable for purifying fluorine and phosphorus wastewater related to the fields of coal chemical industry, solar energy, semiconductors and the like, wherein the treatment process is simple, corresponding reaction units can be increased or decreased according to the actual situation of project emission standards, all reaction tanks are compactly arranged, the land is saved, and the operation and maintenance cost is low.