Here, a new shutdown control system for the nanofiltration (NF) process is proposed to alleviate flushing due to reverse flow caused by the osmotic pressure. The non-reverse flow shutdown control of the multi-stage NF membrane can be achieved through the following steps: (1) refluxing the product water to replace the inlet water; (2) maintaining the high-pressure pump at a constant pressure; (3) sequentially closing the boost pump and the supporting valve; (4) closing the high-pressure pump and the control valve; (5) closing the flushing pump and the control valve. This novel control system was applied to an industrial NF membrane separation system with zero liquid discharge at the Shaanxi Yanchang Coal Yulin Energy and Chemical Co. Ltd., China, and exhibited high stability. Compared with the traditional control strategy, the cost of water treatment was reduced by 0.0029 $/m3, and the produced water increased by 1180 m3 per year for a feed rate of 50 m3/h. The reported methodology, which can improve the long-term process stability and extend the membrane life, shows great potential toward implementation in full-scale NF applications.