The prominent advantage of meshfree method, is the way to build the representation of computational domain, based on the nodal points without any explicit meshing connectivity. Therefore, meshfree method can conveniently process the numerical computation inside interested domains with large deformation or inhomogeneity. In this paper, we adopt the idea of meshfree representation into cardiac medical image analysis in order to overcome the dificulties caused by large deformation and inhomogeneous materials of the heart. In our implementation, as element-free Galerkin method can eficiently build a meshfree representation using its shape function with moving least square fitting, we apply this meshfree method to handle large deformation or inhomogeneity for solving cardiac segmentation and motion tracking problems. We evaluate the performance of meshfree representation on a synthetic heart data and an in-vivo cardiac MRI image sequence. Results showed that the error of our framework against the ground truth was 0:1189 ± 0:0672 while the error of the traditional FEM was 0:1793 ± 0:1166. The proposed framework has minimal consistency constraints, handling large deformation and material discontinuities are simple and efficient, and it provides a way to avoid the complicated meshing procedures while preserving the accuracy with a relatively small number of nodes.