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This paper proposes a fault estimation (FE) based fault-tolerant control (FTC) strategy to maintain system reliability and achieve desirable control performance for a 3-DOF helicopter system with both actuator drift and oscillation faults and saturation. The effects of the faults and saturation are combined into a composite non-differentiable actuator fault function, which is approximated by a differentiable function and estimated together with the system state using a nonlinear unknown input observer. An adaptive sliding mode controller based on the estimates is developed to compensate the effects of the faults and saturation. Taking into account the bi-directional robustness interactions between the FE and FTC functions, an integrated design approach is proposed to obtain the observer and controller gains in a single-step so as to achieve robust overall FTC system performance. In fault-free cases, the proposed strategy can be considered as a new approach for anti-windup control to compensate the effect of input saturation. Comparative simulations are provided to verify the effectiveness of the proposed design under different actuator fault scenarios.