Abstract: A novel control scheme combining the nonlinear track differentiator and extended state observer (ESO) was presented for a class of chaotic systems with non-affine inputs. All uncertainties and external disturbances were modeled in backstepping. The nonlinear track differentiator was employed to approximate the derivative of the virtual control or the reference signals. The ESO was employed to estimate the uncertainties and disturbance in the system,furthermore, the convergence of ESO was proved. The main characteristics of the scheme are that the computation time is much less than other approaches presented in references and the tracking errors are guaranteed to be uniformly asymptotically stable. Foremost, the output of chaotic system can track arbitrary differentiable reference signal. Simulation results of chaotic systems with non-affine inputs, modeled uncertainties and external disturbances illustrate the feasibility and effectiveness of the proposed control method.