The unconventional emergency needs to be dealt with from the perspective of baseline. That is, we need to study problems based on the worst scenario. Thus, the paper formulated a two-level robust optimization model to solve the coordination problem arising from the relief distribution and transportation. The topline model determines the optimal distribution of emergency resource from the perspective of cost minimization, while the baseline model is to transport and distribute based on the distribution policy of topline from the perspective of time saving, in order to realize the coordinate optimization of emergency resource allocation timely and efficiently, and reduce most the loss of disaster. The model described the scarcity of relief demand and converted the coordination problem into two connected problems. Finally, the numerical analysis demonstrated the coordination value and robustness of the distribution policy. Besides, robust approach helps improve the equity of distribution plan.