A medical image fusion method based on bi-dimensional empirical mode decomposition (BEMD) and dual-channel PCNN is proposed in this paper. The multi-modality medical images are decomposed into intrinsic mode function (IMF) components and a residue component. IMF components are divided into high-frequency and low-frequency components based on the component energy. Fusion coefficients are achieved by the following fusion rule: high frequency components and the residue component are superimposed to get more textures; low frequency components contain more details of the source image which are input into dual-channel PCNN to select fusion coefficients, the fused medical image is achieved by inverse transformation of BEMD. BEMD is a self-adaptive tool for analyzing nonlinear and non-stationary data; it doesn’t need to predefine filter or basis function. Dual-channel PCNN reduces the computational complexity and has a good ability in selecting fusion coefficients. A combined application of BEMD and dual-channel PCNN can extract the details of the image information more effectively. The experimental result shows the proposed algorithm gets better fusion result and has more advantages comparing with traditional fusion algorithms.