For the high-demand operating safety and flight safety, the hysteresis dead-zone as a health indicator (HI) related to backlash abrasion is proposed for health monitoring and prediction of aircraft mechanical control systems (MCSs). First, a multi-backlash mass-damper-spring (MDS) model is built for MCSs degradation simulation to demonstrate the HI’s validity. Then, by comparing with Prandtl-Ishlinskii (PI), generalized PI (GPI), and Preisach model, the Backlash-like-PSO model gets the best results on criteria of correlation index (R2) and root mean square error (RMSE). The Backlash-like-PSO model is innovatively adopted for HI extraction. Finally, compared with several generally used approaches, the Gaussian process regression (GPR) approach is designated for the MCSs degradation prediction based on HI, depending on its better prediction accuracy and smoother degradation trend by performance estimation on RMSE, R2, etc. The effectiveness and feasibility of the proposed method are validated by the practical flight data.