Abstract: The primary flight feathers, secondary flight feathers, tail feathers and down feathers of Grus nigricollis and Grus grus were microscopically imaged, and the morphological data were determined and compared by statistical analysis. The quantitative indexes of morphological structure were statistically analyzed by single factor analysis and sample t test, and the Fisher discriminant function of characteristic indexes was established. The results were showed as following: the length of the barb in the inner web of remiges feathers, the angle between the barb in the inner web of tail feathers and the area of the accessory pinna of a primary flight feather, are remarkably different between G. nigricollis and G. grus in the terms of macrostructure; the number of cilia couples and ventral teeth from distal barbules in secondary flight feathers, the number of ventral teeth in proximal barbules of remiges feathers, the number of hamuli from distal barbules in tail feathers, the distance between nodular and diameters of nodular between the 2 kinds of Grus in the terms of microstructure also showed significantly different; macroscopic and microscopic characteristics of the Grus feathers were quantitatively analyzed, and Fisher discriminant function based on the difference index was constructed. The accuracy rate of using back substitution method to test the discriminant equation is 80.2%. It suggested that Grus of primary and secondary flight feathers and tail feathers of sample classification can be achieved by the number of hamuli, cilia couples, ventral teeth from distal barbules, the number of ventral teeth in proximal barbules, the angle between the barb in the inner web, the length of the barb in the inner web of remiges feathers, the area of the accessory pinna and Length of a feather shaft. It further enriches the identification methods or approaches of rare crane species in China.