The functionality of biomolecules depends on their flexible structures, which can be characterized by their surface shapes. Tracking the deformation and comparing biomolecular shapes are essential in understanding their mechanisms. In this paper, a new spectral shape correspondence analysis method is introduced for biomolecules based on volumetric eigenfunctions. The eigenfunctions are computed from the joint graph of two given shapes, avoiding the sign flipping and confusion in the order of modes. An initial correspondence is built based on the distribution of a shape diameter, which matches similar surface features in different shapes and guides the eigenfunction computation. A two-step scheme is developed to determine the final correspondence. The first step utilizes volumetric eigenfunctions to correct the assignment of boundary nodes that disobeys the main structures. The second step minimizes the distortion induced by deforming one shape to the other. As a result, a dense point correspondence is constructed between the two given shapes, based on which we approximate and predict the shape deformation, as well as quantitatively measure the detailed shape differences.