In the egg market, due to the different nutritional values of eggs laid by hens under different feeding conditions, it is common for low-quality eggs to be counterfeited as high-quality eggs. This paper proposes a residual dense comprehensively regulated convolutional neural network (RDCR-Net) to identify the quality of eggs laid by hens under different feeding conditions. Firstly, a hyperspectral system is used to obtain the spectral information of eggs. Secondly, due to the complex structure of the spectral information, a comprehensively regulated convolution (CRConv) is proposed to extract features hidden in the spectral information through feature transformation in multiple spaces. Thirdly, due to the limited availability of spectral information training samples, deep networks may suffer from feature degradation. The residual dense comprehensively regulated block (RDCR-Block) is proposed to tightly connect multiple CRConv layers with residual dense connections. Finally, the RDCR-Block is taken as the central unit, and the RDCR-Net is designed to identify egg spectral information. In the comparison of multi-model results, the RDCR-Net obtains the best classification performance with 96.29% accuracy, 97.53% precision, 97.14% recall, and 96.19% kappa coefficient. In summary, the RDCR-Net effectively extracts the deep features of spectral information, achieves high accuracy in identifying eggs laid by hens under different feeding conditions, and provides a new method for egg quality traceability.