A novel terminal guidance system with a pulse-width-pulse-frequency (PWPF) modulator based on variable dead zone is designed for exo-atmospheric kill vehicle (EKV). At first, a three dimensional (3D) missile-target engagement kinematics is established on the line-of-sight (LOS) coordinate system, the guidance law is compensated by estimated maneuvering acceleration of target from nonlinear disturbance observer (DO). Secondly, a 3D terminal sliding mode guidance law with gradually increasing robustness is proposed for EKV, and the finite time stability of closed system is strictly proven. A PWPF modulator with variable dead zone is proposed to resist the sensitivity of LOS angle with relative distance decreasing, and the stability of modulator is proven by describing function technique. Finally, the guidance performances are assessed through a numerical simulation, the proposed guidance law is better attack precision than traditional guidance law, and the PWPF modulator with variable dead zone is more reasonable in fuel allocation and smaller on miss distance than traditional PWPF modulator.