The control problem for the trajectory tracking of a flexible two-link manipulator incorporating a payload described by a nonlinear model is addressed in the present work. The influence of parametric variation of system attributes on the design of PD inversion-based nonlinear control of a two-link manipulator has been demonstrated. The kinetic energy expression for the system is obtained by using the position vector in generalized coordinate system. The Euler-Lagrange's approach in conjunction with the assumed mode method is utilized to obtain the dynamic model of the system composed of four nonlinear ordinary differential equations which are simulated, and the results have been graphically illustrated. The effect of system parameters such as payload mass, joint mass, system inertia, and physical and geometric properties of the links are explored by comparing the simulation outcomes. Moreover, the presented results exhibit that the system parameters have a significant effect on the input-output characteristics and should be accounted for while designing such systems.