The invention discloses a simulated annealing algorithm based frequency spectrum distribution method in a super-dense small cell network. An interference matrix is created by utilizing interference relation among small cell users, an undirected interference relation graph is created according to the interference matrix, a maximal cluster in the interference graph is solved according to a simulated annealing algorithm, points which form the cluster are removed, a maximal cluster is searched again, and the algorithm is stopped until there is no cluster. A frequency spectrum is segmented into sub-bands according to the sum of the amount of clusters and the amount of non-cluster users, and the frequency spectrum is distributed to the users. The method can be used to reduce segmentation of the frequency spectrum substantially, increase the utilization rate of the frequency spectrum, and improve the throughput of the whole network.