The invention provides a method of treating the process effluent of dimethyl ether synthesis via methanol dehydration. The method at least comprises the following three steps: the first step, the process effluent is divided into two flows through the evaporation, wherein one flow is rich in organic substances and the other flow is poor in organic substances; the second step, the flow rich in organic substances is subjected to the membrane separation, the organic substances in the concentrate is recovered, and the water phase is reutilizes; and the third step, the flow poor in organic substances is subjected to the biochemical treatment so that the water quality meets the requirements on reclaimed water. Optionally, the method further comprises the fourth step, that is, the reclaimed water is treated by the water quality stabilization technology to meet the reclaimed water treatment requirement on the production equipment. The method can recycle the whole effluent after treatment and reclaim the organic substances in the effluent, and achieves the effect of resource utilization of the process effluent and the organic substances in the process effluent.