This paper proposes a new trajectory tracking scheme for the constrained nonlinear underwater vehicle-manipulator system (UVMS). For overcoming the unmodeled uncertainties, external disturbances, and constraints of control inputs in the operation of UVMS, a modified constrained H∞ controller with a basic computed-torque controller (CTC) and a new designed nonlinear disturbance observer (NDO) are proposed. The CTC gives the nominal model-based control. The NDO is designed based on the system dynamics and used to online provide the estimation of the lumped disturbances. However, the designed NDO is an observer of biased estimation, i.e., it has a blind domain of disturbance estimation which cannot be rejected. In order to reject the biased estimation, the modified constrained H∞ controller is designed but with new features. To the best of our knowledge, the conventional H∞ robust controller is generally designed by calculating the Riccati equation offline and ignoring the constraints of control inputs made by the physical actuators, which are poor in handling the time-varying environment. In order to solve these issues, the modified constrained H∞ robust controller online optimized by grey wolf optimizer (GWO) is designed to ensure the control system has a compensation of the biased estimation, a satisfied constrained control input, and a fast calculation. In this paper, we modify the prior method of offline calculating the Riccati equation of the conventional H∞ robust controller to be an online optimization scheme and proposed a new constrained evaluation function. The new constrained evaluation function is online optimized by the GWO, which can both find out the constrained suboptimal control actions and compensate the biased estimation of the NDO for the UVMS. The whole system stability is proved. The effectiveness of the fast online calculation, tracking accuracy, and lumped disturbances rejection is shown by a series of UVMS simulations.