In this paper, a multi-level method has been adopted to optimize the holes machining process with genetic algorithm (GA). Based on the analyzing of the features of the part with multi-holes, the local optimal processing route for the holes with the same processing feature is obtained with GA, then try to obtain the global optimal route with GA by considering the obtained local optimal route and the holes with different features. That is what the multi-level method means. The optimal route means the minimum moving length of the cutting tool and the minimum changing times of the cutting tool. The experiment is carried out to verify the algorithm and the proposed method, and result indicates that with GA and using the multi-level method the optimal holes machining route can be achieved efficiently.