There are many kinds of optimization algorithms and they have widely application. It is of great significance to select suitable optimization algorithms when solving complex problems such as global large-scale combinatorial optimization. The application of simulated annealing algorithm in solving the shortest path problem of aircraft cruise is mainly analyzed. And it is compared with genetic algorithm and improved genetic algorithm. The conclusion shows that simulated annealing algorithm has the shortest path in the application of the shortest path, and has better solution results than other two optimization algorithms. Therefore, simulated annealing algorithm plays an important role in solving complex global optimization problems.