Cryo-electron microscopy (CryoEM) is a very important method for studying the structures of macromolecules. Structure fitting is one of the key problems in CryoEM technique. We propose a novel structure fitting method for automatic alignment of the atomic model and CryoEM density map. Based on the domain knowledge, 3D density map is presented by local maximum points. And the atomic model is presented by atoms with high density value. According to characteristic of CryoEM density map, these atoms must correspond to one of the local maximum, then employ absolute orientation algorithm to calculate the rotation matrix and transfer vector. To show the efficiency of our method, we apply the algorithm on two pairs of test data.