This paper presents a novel Lyapunov function-based backstepping controller design to tackle the tracking problems for nonlinear systems with unmodeled dynamics and unmeasurable states. The coexistence of unmodeled dynamics and unmeasurable states is the main challenge, which calls for novel techniques to take these two factors into account simultaneously. First, the classical Luenberger observer is extended with a novel transformation function to decouple the original system state and state estimation error. In this way, the effect of unmodeled dynamics on system stability can be separately considered. On this basis, a command-filtered controller is designed to simplify the backstepping design procedures. It is worthy to pointed out that, a novel Lyapunov function is developed to simplify the stability analysis with command filter, where the filter errors, the observer error, compensated tracking errors, and parameter estimation errors can be guaranteed to be semi-globally uniformly ultimate bounded. The simulation studies are investigated to validate the effectiveness of the presented design scheme.