Scattering hyperspectral technology is a nondestructive testing method with many advantages. Here, we propose a method to improve the accuracy of egg freshness, research the influence of incident angles of light source on the accuracy and explain its mechanism. A variety of weak classifiers classify eggs based on the spectra after preprocessing and feature wavelength extraction to obtain three classifiers with the highest accuracy. The three classifiers are used as metamodels of stacking ensemble learning to improve the highest accuracy from 96.25% to 100%. Moreover, the highest accuracy of scattering, reflection, transmission and mixed hyperspectral of eggs are 100.00%, 88.75%, 95.00% and 96.25%, respectively, indicating that the scattering hyperspectral for egg freshness detection is better than that of the others. In addition, the accuracy is inversely proportional to the angle of incidence due that the smaller the incident angle, the camera collects a larger proportion of scattering light, which contains more biochemical parameters of an egg than that of reflection and transmission. These results are very important for improving the accuracy of non-destructive testing and selecting the incident angle of the light source, and have potential applications in online non-destructive testing.