In order to effectively improve the pathological diagnosis capability and feature resolution of 3D human brain CT images, a threshold segmentation method of multi-resolution 3D human brain CT image based on edge pixel grayscale feature decomposition is proposed in this paper. In this method, first, original 3D human brain image information is collected, and CT image filtering is performed to the collected information through the gradient value decomposition method, and edge contour features of the 3D human brain CT image are extracted. Then, the threshold segmentation method is adopted to segment the regional pixel feature block of the 3D human brain CT image to segment the image into block vectors with high-resolution feature points, and the 3D human brain CT image is reconstructed with the salient feature point as center. Simulation results show that the method proposed in this paper can provide accuracy up to 100% when the signal-to-noise ratio is 0, and with the increase of signal-to-noise ratio, the accuracy provided by this method is stable at 100%. Comparison results show that the threshold segmentation method of multi-resolution 3D human brain CT image based on edge pixel grayscale feature decomposition is significantly better than traditional methods in pathological feature estimation accuracy, and it effectively improves the rapid pathological diagnosis and positioning recognition abilities to CT images.