Traditional clonal selection algorithm gives us some inspiration for many applications, but in the medical image enhancement application we found some defects of this algorithm. So we improved the clonal selection algorithm in three ways. First, we designed the real coding of the MRI brain image, instead of binary coding. Second, we added the mutation distance to control the mutation progress and avoid only the local optimization. In addition, we adjust the clone selection and the mutation together in the Gauss distribution, the uniform distribution, and the chaotic distribution, rather than in only the Gauss distribution. Then we use the real MRI brain images to test the image enhancement of our improved clonal selection algorithm. The experimental results show that our approach outperform the median filtering (MF) and the adaptive template filtering (ATF) in enhancing the MRI brain images.