Thrust allocation serves as a critical means for achieving vector propulsion in unmanned surface vessels (USV) equipped with dual waterjet thrusters. However, existing thrust allocation methods employed in vessels featuring azimuth thrusters fail to address the resolution of vector forces for dual waterjet propulsion, due to characteristics such as thrust angle limitations and reverse thrust. To achieve vector motion control of a dual waterjet propelled USV, a hierarchical optimization-based thrust allocation algorithm is proposed. In the first tier, a vector synthesis approach incorporating enhanced angle constraints is utilized to acquire top-tier vector thrust satisfying constraints on the rotating range and rate characteristics of the thrusters. In the second tier, leveraging the top-tier vector thrust values as inputs and considering constraints on thruster power and power change frequency, an optimization method based on seeking minimal distance is proposed. This method facilitates the allocation of reverse thrust angles and nozzle flow velocities for waterjet thrusters, thereby resolving singular issues in dual waterjet thrust allocation. Simulation experiments and the semi-physical simulation experiments validate the effectiveness of the hierarchical optimization-based thrust allocation algorithm for dual waterjet thrusters. Results indicate that hierarchical optimization effectively achieves thrust allocation for dual waterjet thrusters, while concurrently limiting fluctuations in thruster power frequency and amplitude during expected thrust variations, thereby reducing shafting wear while achieving target vector thrust.