In this paper, we study the controllability of multiagent systems under equitable partition and automorphism. For the different number of communication links between nontrivial cells, there are two classes of nontrivial cells, one is complete connected nontrivial cells, another is incomplete connected nontrivial cells, which takes different affections on controllability. The nontrivial cells with odd nodes and even nodes also take different affections on controllability. Assume there are automorphisms of graph G, then if the positions of the entries in eigenvector x of L are changed, it still be the eigenvectors of L, so that there are some eigenvector x existing 0 entries, and we can analyze the controllability by studying the position of zero entries. Besides, by equitable partition and automorphism, we give new necessary conditions for controllability of multi-agent systems.