This paper investigates the position and velocity tracking control of a class of high-speed trains (HST) with unknown actuator failures (AF) and control input saturation (CIS). Firstly, a nonlinear dynamic model for HST at normal operating status is built. The structure of traction system in HST is analyzed and the corresponding model for HST with unknown AF is presented as well. The type of AF under consideration is that some of the plant inputs are influenced by hopping function. An adaptive model-based fault detection and diagnosis (AMFDD) module is proposed based on immersion and invariance (I&I) method to make decisions on whether a fault has occurred. A new framework to design a monotone mapping is proposed in I&I method, that is,P(x)-monotone. Using on-line obtained fault information, an adaptive law is designed to update the controller parameters to handle unknown AF and CIS in HST simultaneously when some of plant parameters are unknown. Closed-loop stability and asymptotic position and velocity tracking are ensured. Numerical simulations of China Railways High-speed 2 (CRH2) train are provided to verify the effectiveness of the presented scheme.