In recent years, fused images have been developed for fast processing of medical images, which provide a more reliable basis for reducing the burden on physicians because they can contain multiple times the image information. In order to achieve fast and accurate recognition results in medical image recognition, avoid similar blocks and shadow fitting in CT/MR fusion images, and improve the entire medical system, in this study, CT/MRI image fusion of brain images is studied based on algorithms generated by Convolutional Neural Network (CNN). The study utilizes Rolling Guidance Filter (RGF) to divide medical CT/MRI images into two parts, one of which is used for model training and the other for image fusion. In the experiments, the results of all three experiments are compared with the Nonsub Sampled Contourlet Transform -Piecewise Convolutional Neural Network (NSCT -PCNN), and the CNN-RGF MI/ IE/SSIM/AG values of CNN-RGF are superior compared to the conventional algorithm of NSCT-RCNN with an average improvement of 10.0% and above, and the resulting CNN-RGF observed meningitis, hydrocephalus, and cerebral infarction with an average of 24.8% higher compared to NSCT-RCNN. The outcomes show that for brain image fusion and detection, the CNN-RGF approach put forward in the study performs better.