The invention discloses a comprehensive desalting recovering method and system of MEG saline wastewater. The method comprises the following steps: dehydrating and concentrating the MEG saline wastewater in a multi-level membrane distilling-crystallizing process, when the concentration of the salt in the MEG saline wastewater reaches the hyper-saturated state, adding a certain amount of seed crystals into a crystallizing kettle to induce the salt in the MEG saline wastewater to separate out in certain size distribution, so that the MEG concentration and recovery, the high-purity infiltration water recovery and the inorganic salt crystal recovery with specific size distribution can be synchronously processed, the zero discharge of the MEG saline wastewater can be reached and the comprehensive utilization value of the MEG saline wastewater can be increased. The processed raw material is a rich liquid raw material or a barren liquid raw material, the temperature of the processed raw material is 45-80 DEG C, and the transportation flow rate of the raw material is 0.2-3 m/s. The operation flow is continuous operation or intermittent operation. The direct contact membrane distillation or vacuum membrane distillation can be used in the membrane distillation process.