The invention relates to a treatment method of waste water containing organic phosphorus, comprising the following steps: leading process waste water containing organic phosphorus to pass through a sand filtration tank for removing suspended matter and then adjusting the pH value thereof to 3-4; leading the process waste water to pass through a high-efficient catalytic oxidation apparatus, adding hydrogen peroxide for conducting oxidative degradation of the process waste water; then introducing the process waste water to a catalytic micro-electrolysis device, adding scrap iron and activated carbon and stirring, conducting electrochemical reaction, blasting air into the lower part of the catalytic micro-electrolysis device, and removing hard-degradable organic matter in the process waste water; and introducing the effluent of the catalytic micro-electrolysis device into an oxidation kettle, adding hydrogen peroxide for conducting multistage oxidation treatment, later adding lime, adjusting the pH value of the process waste water to 8-9, then adding flocculant for conducting precipitation, and forming ironic phosphate and calcium phosphate precipitate, thus removing phosphorus in the waste water. Compared with the prior art, the treatment method transforms the organic phosphorus into inorganic phosphorus for removal and has high removal rate of total phosphorus and low running cost, and the formed phosphate can be recycled and reused.