<p>Aero-engine performance degradation may lead to key parameters surpassing their predefined safety limits, thereby posing significant operational risks that may compromise flight safety and engine longevity. To sustain thrust output under overlimit operating conditions, a novel limit protection control (LPC) method for variable cycle engines (VCEs) is proposed, which incorporates overlimit prediction with proactive switching mechanisms, enabling rapid and stable control under overlimit conditions. First, the Monte Carlo simulations are conducted to identify the parameters prone to exceeding safety thresholds in deteriorated engine conditions. Subsequently the control variable governing the LPC loop is determined through sensitivity analyses. Overlimit prediction and model-inverse limit protection control based on the neural network state space equation (NSSE) are proposed to pre-emptively trigger the LPC loop when a predicted breach of safety constraints is detected. By integrating the LPC and the main thrust control loops, the overall control system can respond effectively to both normal operational conditions and overlimit scenarios, providing a comprehensive solution for engine control under degraded performance. Simulation results show that compared with the proportional–integral LPC method employing min–max selection logic, the overlimit prediction and protection control framework based on the NSSE can detect an impending overlimit situation and swiftly activate the LPC loop. The limit protection loop and the main control loop operate synergistically, demonstrating that the LPC strategy proposed effectively mitigates overlimit risks and improves system dynamic performance under deteriorated engine conditions.</p>