Ammonia shows great potential as a zero-carbon fuel for vehicles. However, both the internal combustion engine (ICE) and the proton exchange membrane fuel cell (PEMFC), the currently available vehicle engines, require hydrogen decomposed from ammonia. On-board hydrogen production is an energy-intensive process that significantly reduces system efficiency. Therefore, energy recovery from residual heat is essential to promote overall efficiency, but ICE and FC require different amounts of hydrogen, and produce residual heat of dissimilar quality and quantity. To thoroughly understand the relationships among system configuration, rate of residual heat recovery and system efficiency, this paper takes three typical ammonia-fueled power systems, which employs only ICE, only PEMFC and both ICE and PEMFC as engine(s), respectively, as examples to set up system efficiency model and conduct simulation under various operating conditions. Results show there is a mismatch between the produced residual heat and the heat required for ammonia decomposition for systems using only ICE or PEMFC. For system using both PEMFC and ICE, the residual heat can be recovered to a maximum extent by way of parameters matching and dynamic power management between engines. This system has the highest efficiency and widest high efficiency region among the three analyzed typical configurations.