Self-assembly reveals the essence of DNA computing, DNA self-assembly is thought to be the best way to make DNA computing transform into computer chip. This paper introduce a method of DNA 3D self-assembly algorithm to solve the Maximum Clique Problem. Firstly, we introduce a non-deterministic algorithm. Then, according to the algorithm we design the types of DNA tiles which the computation needs. Lastly, we demonstrate the self-assembly process and the experimental methods which could get the final result. The computation time is linear, and the number of the distinctive tile types is constant.