The two-inertia system with variable-length flexible load (TSVFL) is a typical dynamic model uncertain system. It is affected by transmission flexibility, flexible load length variation, and inaccurate friction torque, in which the flexible load will vibrate during rotation. In this study, a neural network compensation sliding mode control (SMC) strategy mixed with the angle-independent method (AIM) is proposed to suppress the vibration of the TSVFL. Among them, the AIM is proposed to design the fluctuating desired input of the motor. The vibration of the flexible load is offset by the speed fluctuation of the motor. The RBF neural networks are proposed to recognize the uncertain term in the TSVFL's dynamic model. First, the nonlinear mathematical model of the TSVFL is deduced based on the assumed mode method. Then, the Lyapunov stability theorem is proposed to design the weight coefficients’ adaptive law in neural networks and the robust term in the control law. Finally, simulation and physical experiments on output speed control are implemented. The results show that the proposed strategy is able to effectively decrease the error and weaken the vibration.