As a power generation device, direct ammonia protonic ceramic fuel cells (NH3–PCFCs) also produce a significant amount waste heat, which not only results in energy wastage but also abnormal operation if the waste heat is not removed. To address these concerns and enhance generation electricity capacity, a novel waste heat recovery system based upon NH3-PCFC and alkali metal thermal electric converter (AMTEC) is first proposed, wherein the AMTEC converts the high-grade exhaust heat produced by the NH3-PCFC to extra electricity. Considering ammonia decomposition sluggish kinetics, various irreversible overpotential losses of NH3-PCFC as well as thermodynamic losses within the integrated system, the energetic/exergetic performance parameters evaluating the NH3-PCFC, AMTEC and the hybrid system are formulated. The general performance characteristics of the proposed system are revealed, along with a sensitive analysis conducted under specific operational conditions or structural parameters. Numerical calculation exhibited that the maximum attainable power density of the hybrid system has been promoted 20.5 % than that of stand-alone NH3-PCFC system. The multi-objective genetic algorithm is utilized to optimize the hybrid system performance for trade-off the power output and efficiency. Optimized results show the power density and corresponding efficiency of proposed system can respectively reach 6762.3 W m−2 and 49.8 % in the corresponding optimization conditions.