Abstract: Membrane separation was applied for the desalination of pilot collagen extraction from fish scale. The effect of ultrafiltration membranes with different MWCO or different material on the desalination rate and collagen recovery rate were researched. The result showed that the optimal membrane was spiral ultrafiltration membrane with MWCO 8ku, the waste water could be recycled for desalination process after treated by nanofiltration membrane. The results of three pilot batch tests of the collagen extraction desalination showed that when the collagen extraction was four times concentrated, the collagen recovery rate was more than 75%, the removal rate of inorganic salt related to ash in the extraction was more than 85%, the ash content in the final collagen product was less than 1%.