In order to overcome the problems that a process of extracting and refining long chain binary acid in the prior art is complex, high in energy consumption, bad in product quality and the like, the invention provides a water phase melt crystallization process for long chain binary acid. The problem of using an organic solvent in the extraction process in the prior art is solved, impurity content such as proteins and pigment substances in the product are reduced effectively, and the purity of the crystallized long chain binary acid product can be greater than 99wt%.