This paper presents a novel approach based on spectral geometry to quantify and visualize non-isometric deformations of 3D surfaces by mapping two manifolds. The proposed method can determine multi-scale, non-isometric deformations through the variation of Laplace-Beltrami spectrum of two shapes. Given two triangle meshes, the spectra can be varied from one to another with a scale function defined on each vertex. The variation is expressed as a linear interpolation of eigenvalues of the two shapes. In each iteration step, a quadratic programming problem is constructed, based on our derived spectrum variation theorem and smoothness energy constraint, to compute the spectrum variation. The derivation of the scale function is the solution of such a problem. Therefore, the final scale function can be solved by integral of the derivation from each step, which, in turn, quantitatively describes non-isometric deformations between two shapes. To evaluate the method, we conduct extensive experiments on synthetic and real data. We employ real epilepsy patient imaging data to quantify the shape variation between the left and right hippocampi in epileptic brains. In addition, we use longitudinal Alzheimer data to compare the shape deformation of diseased and healthy hippocampus. In order to show the accuracy and effectiveness of the proposed method, we also compare it with spatial registration-based methods, e.g., non-rigid Iterative Closest Point (ICP) and voxel-based method. These experiments demonstrate the advantages of our method.