The unique fingerprints of radio frequency (RF) devices play a critical role in enhancing wireless security, optimizing spectrum management, and facilitating device authentication through accurate identification. However, high‐accuracy identification models for radio frequency fingerprint (RFF) often come with a significant number of parameters and complexity, making them less practical for real‐world deployment. To address this challenge, our research presents a deep convolutional neural network (CNN)–based architecture known as the separation and fusion convolutional neural network (SFCNN). This architecture focuses on enhancing the identification accuracy of RF devices with limited complexity. The SFCNN incorporates two customizable modules: the separation layer, which is responsible for partitioning the data group size adapted to the channel dimension to keep the low complexity, and the fusion layer which is designed to perform deep channel fusion to enhance feature representation. The proposed SFCNN demonstrates improved accuracy and enhanced robustness with fewer parameters compared to the state‐of‐the‐art techniques, including the baseline CNN, Inception, ResNet, TCN, MSCNN, STFT‐CNN, and the ResNet‐50‐1D. The experimental results based on the public datasets demonstrate an average identification accuracy of 97.78% among 21 USRP transmitters. The number of parameters is reduced by at least 8% compared with all the other models, and the identification accuracy is improved among all the models under any considered scenarios. The trade‐off performance between the complexity and accuracy of the proposed SFCNN suggests that it is an effective architecture with remarkable development potential.