With the rapid development of the economy and society, the water supply-demand conflict in the Xinjiang region has become increasingly prominent, Seawater desalination technology, as the main method for expanding freshwater resources in coastal and arid regions, can effectively alleviate the water supply-demand conflict. Currently, there have been small-scale pilot studies on the desalination of underground brackish water, however, research on the desalination of agricultural salt-alkali drainage is rarely reported. For this purpose, a micro-flocculation medium filtration-ultrafiltration-reverse osmosis coupling process was developped through small-scale comparison and software simulation optimization, and conducts pilot-scale verification. The operational results show that the reverse osmosis device maintains stable water quality during operation, with small fluctuations in the feed pressure, which remains between 10.5×10⁵~15.96×10⁵ Pa, and the system recovery rate is maintained at around 71%, with the product water conductivity fluctuating between 150~350 μS/cm, and the overall desalination rate reaching over 97.04%. The photovoltaic-grid coordinated dynamic power supply mode effectively reduces the operational energy consumption of the desalination system, with the overall operational cost controlled below 0.62 yuan/m³. This pilot application further establishes a technical system for the desalination of agricultural salt-alkali drainage, providing a reference and guidance for the development and utilization of such water sources.