With the consideration of the multi-grade proactive attacks, the problem of reliable network design of third-party logistics(3PL) is studied. A multi-level optimization model of the problem is established, for which, the model of 3PL network design minimizes the total logistics costs subjective to the reliability constraint by opening logistics facilities of different secure grades, the model of proactive attacks minimizes the service level of the network by selecting the attack strategies of different grades, and the model of the network-flows decision maximizes the service level of the network after attacks. According to the characteristic of the model, an improved two-level artificial bee colony(ABC) algorithm is developed. The top-level ABC is used to solve the problem of 3PL network design, and the down-level ABC is used to solve the problem of proactive attacks optimization. The problem of the network-flows decision is solved by using the network-flows algorithm. Finally, numerical experiments are presented and the results show the reasonability of the model as well as the effectiveness of the proposed algorithm.