A method for collaborative and optimal allocation of a route time slot and a flight level comprises: acquiring planned route information and alternative route information in a traffic limited airspace, available time slot information of a downstream airspace unit of the planned route, and flight operation information first, then formulating an algorithm for the collaborative and optimal allocation of the route time slot and the flight level, establishing an objective function and a constraint condition which meet effectiveness by taking a minimum total ground delay loss of all flights, a minimum change number of flight levels of all flights and a minimum total fuel consumption of all flights as objectives, further establishing a multi-objective optimization model for the collaborative allocation of the route time slot and the flight level, and forming a strategy for the collaborative and optimal allocation of the route time slot and the flight level.