Aiming at allocating limited resources of weapons and equipment system reasonably for multi military tasks, the algorithm of tree structure optimizing and configuring resources based on dynamic programming and tree structures is proposed. Introduce problems of weapon and equipment resource allocation, and use dynamic programming tree structure method in weapon and equipment system resource optimal allocation. Go through every military task and resource allocation plan set, take the tactic scheme operation effectiveness value as the final evaluation index, carry out scheme effectiveness sequencing, and help commander to make tactic scheme, realize optimal allocation of weapon and equipment system operation resource, carry out algorithm validation by example analysis. The analysis results show that the optimal algorithm procedure are simple, clear, with simple calculation model, it is practical and feasible.