Flexible lander, composed of multiple nodes connected by flexible material, can reduce the bouncing and overturning during the asteroid landing. To satisfy the complex constraints in the node cooperation of the flexible landing, an intelligent cooperative guidance method is proposed. The method consists of a double-layer cooperative guidance structure, a guidance parameter determination approach, and an action priority strategy. The double-layer contains a basic guidance used to satisfy the terminal state constraints, and a compensatory guidance used to satisfy the lander’s attitude constraint. For the compensatory guidance, the parameters are determined by multi-agent system, which are trained according to the performance index of flexible landing trajectories. The action priority strategy is used to reduce the detrimental effect of parameter inconsistency on the node cooperation. The simulation of flexible landing shows that the cooperative guidance method is effective in improving the landing accuracy while satisfying the constraints. Meanwhile, the method is robust to the disturbance in the navigation and control.