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Abstract Target detection based on hyperspectral images refers to the integrated use of spatial information and spectral information to accomplish the task of localization and identification of targets. There are two main methods for hyperspectral target detection: supervised and unsupervised methods. Supervision method refers to the use of spectral differences between the target to be tested and the surrounding background to identify the target when the target spectrum is known. In ideal situations, supervised object detection algorithms perform better than unsupervised algorithms. However, the current supervised object detection algorithms mainly have two problems: firstly, the impact of uncertainty in the ground object spectrum, and secondly, the universality of the algorithm is poor. A hyperspectral target detection framework based on 3D–2D CNN and transfer learning was proposed to solve the problems of traditional supervised methods. This method first extracts multi-scale spectral information and then preprocesses hyperspectral images using multiple spectral similarity measures. This method not only extracts spectral features in advance, but also eliminates the influence of complex environments to a certain extent. The preprocessed feature maps are used as input for 3D–2D CNN to deeply learn the features of the target, and then, the softmax method is used to output and obtain the detection results. The framework draws on the ideas of integrated learning and transfer learning, solves the spectral uncertainty problem with the combined similarity measure and depth feature extraction network, and solves the problem of poor robustness of traditional algorithms by model migration and parameter sharing. The area under the ROC curve of the proposed method has been increased to over 0.99 in experiments on both publicly available remote sensing hyperspectral images and measured land-based hyperspectral images. The availability and stability of the proposed method have been demonstrated through experiments. A feasible approach has been provided for the development and application of specific target detection technology in hyperspectral images under different backgrounds in the future.