To solve the trajectory tracking control problem of underwater vehicle-manipulator system (UVMS) under strong nonlinear couplings and complex parametric uncertainties and unknown external disturbance, a nonlinear robust control method based on time delay estimation (TDE) was proposed and investigated in this paper. The core idea of this method is that builds the basic architecture of the controller with TDE, and realizes the online estimation and real time compensation of the complex unknown lumped dynamics for the system. Afterwards, a designed desired dynamic equation is used to regulate the system control performance. Benefitting from the compensation of the unknown lumped dynamics and the model-free nature of TDE, the proposed method has good robustness and practical easy usage. Finally, the effective of the proposed method was demonstrated by comparative numerical simulations with a 9 degree of freedoms (DOFs) UVMS.