On the basis of tiles theory model and the existing self-assembly model, an algorithm based on DNA self-assembly model was presented for maximum clique problem, and the corresponding DAE blocks designed in particular for initial molecular, rules of molecular and the detection of molecular were given. Then, an algorithm for solving maximum clique problem was presented with the biologic operation of fluorescence labeling and gel electrophoresis. The proposed algorithm needs Θ(n2+|E|) types of tiles, and the complexity of experiment operation was Θ(1). This algorithm can reduce the complexity of the experiment, and ensure the ease of experiment and the accuracy of results.