This paper presents simulation study on the effects of the cross-sectional area at the merging region and high pressure compressed airflow rate on the flow energy merger, and their optimum adjustments for the change in the compressed air pressure (P air) in the hybrid pneumatic power system (HPPS). The simulation of energy mixing and merging processes was performed for an innovative energy merger pipe in which the open angle (A) of the air storage tank’s throttle valve and the contraction of the cross-sectional area (CSA) at the merging region of the energy merger pipe can be adjusted for changes in P air. The simulations were carried out using computational fluid dynamics (CFD). The results showed that the exhaust-gas recycling efficiency and the merger flow energy are significantly dependent on the optimal adjustments of A and CSA for the change in P air. The optimal conditions for higher exhaust-gas recycling efficiency and the best energy merging process can be achieved at A of around 25–100% and a CSA of around 5–40% for a full range of P air. Under these conditions, the exhaust-gas recycling efficiency reached approximately 80–88%. Therefore, a vehicle equipped with an HPPS can achieve a level of efficiency that is approximately 40% higher than that of conventional vehicles.