We address the issue of multi-aircraft cooperative strategic trajectory planning in free-route airspace (FRA) in this study, taking into consideration the impact of time-varying and altitude-varying wind forecast uncertainty. A bi-level planning model was established in response to the properties of the wind. The upper level focused on minimizing the flight time, while the lower level aimed to reduce potential conflicts. Meanwhile, a heuristic approach based on conflict severity (CS) within the framework of a cooperative co-evolution evolutionary algorithm (CCEA) was proposed to accelerate the convergence speed in view of the complexity of this optimization issue. In order to conduct the experiments, historical data of 1479 flights over western Chinese airspace were retrieved. The number of conflicts, total flight time, total flight time variance, and deviation were used as indicators to evaluate the safety, efficiency, and predictability of the trajectory. When compared to a trajectory in the structured airspace, the optimal solution was conflict-free and reduced the total flight time by about 17.7%, the variance by 11.7%, and the deviation by 37.5%. Additionally, the contrast with the two-stage model demonstrated that the proposed method was entirely meaningful. The outcome of this survey can provide an effective trajectory-planning method, which is crucial for the sustainable development of future air traffic management (ATM).