The collaboration of a multiple unmanned underwater vehicles (multi-UUVs) system has attracted widespread attention in recent years, as it can overcome the limitations of a single UUV and enhance mission completion efficiency. Oriented towards patrol and exploration missions with multiple waypoints, this paper proposes a balanced mission planning strategy, aiming to improve mission quality while reducing mission time for multi-UUVs. Firstly, due to the uneven performance of the two optimization objectives, a quick initialization screening method is employed specifically for mission quality to reduce the mission space. Secondly, to ensure mission load distribution and collaboration among multi-UUVs, and ease the difficulty in solving the issues of mission allocation and route planning, a balanced bi-level mission planning method based on regional segmentation is proposed. Finally, applicable weight evaluation criteria are utilized to evaluate the feasible solution set and determine the optimal solution. The efficacy of the balanced mission planning strategy is substantiated through comprehensive numerical simulations in a complex 2D marine environment.