The problem of multi-period reliable network design for third-party logistics(3PL) is studied with deliberate attack disruption considered. A multi-level model of 3PL reliable network design is established. The network optimization model optimizes the structure of network in every period, including the opening of the logistics facility and the determination of transportation quantity, to minimize the total costs subjective to reliability constraint. The proactive attack model optimizes the attack strategy in each period to minimize the service level of the network. According to the characteristic of the model, an improved two-level estimation of the distribution algorithm(EDA) is designed. The top-level EDA is used to solve the model of 3PL multi-period network design, while the down-level EDA is used to solve the model of multi-period attack. Finally, several simulation experiments are presented to illustrate the rationality of the model and the effectiveness of the proposed algorithm.