For modern military aero-engine, the serpentine nozzle with aft deck is deployed to meet the requirements of stealth and integrated design. Different from existing studies which emphasize the rectangular nozzles and corresponding infrared radiation impact, the effect of the aft deck angle on flow characteristics of serpentine nozzles with a focus on the internal flow, the shock system, the jet’s evolution, and the performance parameters are systematically investigated in this paper. This study is carried out through three-dimensional numerical simulations, which are validated by the experiment. The results show that the aft deck with different angles has a significant impact on the overall flow characteristics, such as the static pressure and the three-dimensional shock system, as a result of the asymmetry and the contraction/expansion effects on the jet. Specifically, upward-deflected aft decks lead to a re-compression effect and the variation of the internal static pressure value can be up to 7%, whereas for downward-deflected aft decks, the effect on the internal flow can be neglected in under-expansion conditions. In addition, the aft deck angle and the extent of boundary layer separation greatly affect the thrust performance and the vortex evolution, which determines the downstream evolution of the jet cross-section. Effective thrust coefficient is closely tied to the thrust vector angle, with the coefficient reaching its zenith when the thrust vector angle is closest to 0°. This study reinforces understanding of the interrelated problems and may facilitate the development of the optimal aft deck angle for various applications.