The egg production of laying hens is crucial to breeding enterprises in the laying hen breeding industry. However, there is currently no systematic or accurate method to identify low-egg-production-laying hens in commercial farms, and the majority of these hens are identified by breeders based on their experience. In order to address this issue, we propose a method that is widely applicable and highly precise. First, breeders themselves separate low-egg-production-laying hens and normal-laying hens. Then, under a halogen lamp, hyperspectral images of the two different types of hens are captured via hyperspectral imaging equipment. The vertex component analysis (VCA) algorithm is used to extract the cockscomb end member spectrum to obtain the cockscomb spectral feature curves of low-egg-production-laying hens and normal ones. Next, fast continuous wavelet transform (FCWT) is employed to analyze the data of the feature curves in order to obtain the two-dimensional spectral feature image dataset. Finally, referring to the two-dimensional spectral image dataset of the low-egg-production-laying hens and normal ones, we developed a deep learning model based on a convolutional neural network (CNN). When we tested the model’s accuracy by using the prepared dataset, we found that it was 0.975 percent accurate. This outcome demonstrates our identification method, which combines hyperspectral imaging technology, an FCWT data analysis method, and a CNN deep learning model, and is highly effective and precise in laying-hen breeding plants. Furthermore, the attempt to use FCWT for the analysis and processing of hyperspectral data will have a significant impact on the research and application of hyperspectral technology in other fields due to its high efficiency and resolution characteristics for data signal analysis and processing.