The adaptive cycle engine (ACE), with its multi-variable geometry components, can adjust its bypass ratio over a wide range to adapt to different operating conditions. It has become the ideal propulsion system for the next generation of aircraft engines. Currently, there are multiple configurations for ACEs. However, the evaluation of different configurations involves various indicators, making it a multi-objective decision problem. In addition, the quantification of these indicators is challenging. A comprehensive evaluation method based on the Analytic Hierarchy Process (AHP) from the overall engine perspective was established in this paper. Steady-state performance, transient-state performance, structure, and technical risks were considered as evaluation criteria. Simulations and comparative analyses of each evaluation indicator for three typical configurations of ACE were performed and quantified, and then engine evaluations were completed. The evaluation results showed that ACE with a split fan and Core Driven Fan Stage (CDFS) has a larger thrust-to-weight ratio and lighter weight; ACE with Fan on the Blade (Flade) and CDFS maintains better performance in temperature characteristic and power extraction characteristic, as well as greater supersonic cruise thrust and faster deceleration response; ACE with a split fan without CDFS has greater advantages in takeoff thrust, subsonic cruise specific fuel consumption, acceleration time, size, and technical risks, and scores the highest in the comprehensive evaluation model.