The invention discloses a surface source pollution control system based on water-fertilizer high-efficient management. The system comprises a surface source pollution primary treatment unit, a surface source pollution deep treatment unit, a fertilizer application unit, an environment detection unit, a central control unit, a water flow control unit, a mixing and stirring apparatus and a drop irrigation apparatus, wherein the surface source pollution primary treatment unit is used for primarily treating water sourced by a surface source, the environment detection unit is used for detecting an actual condition of soil in real time, the water flow control unit receives an instruction from the central control unit to control the direction of the water flow, and the surface source pollution deep treatment unit is used for deeply treating the water treated by the surface source pollution primary treatment unit. Compared with the prior art, the surface source pollution control system has the beneficial effects that not only can the pollution problem of the agriculture surface source be effectively solved, but also the treated water which is polluted by the surface source is recycled, the water resource is saved, and the high-efficient management of the water fertilizer can be realized according to the actual condition of the soil.