With the aim to investigate the feasibility of near-infrared microscopy method for discrimination of processed animal proteins in feeding stuffs, twelve processed animal protein samples and 14 plant based feed samples were collected. At the same time, four feeds were prepared for validation. The spectra were got with PerkinElmer spotlight 400+spectrum 400 FT-NIR microscope, and the calibration equation was established by partial least squares method with the pretreatment of Savitzky-Golay derivative 1442, full multiplicative scatter correction and average variables 2. The result showed that the calibration gave determination coefficients of 0.969，and a standard error of cross validation of 0.090. The processed animal protein samples could be detected in nature feed samples. The results indicate that near-infrared microscopy has huge potential in detecting the processed animal proteins in feeding stuffs. 