With the rapid development of modern aero engines towards high thrust-to-weight ratio and high efficiency, the design optimization of thermal management systems has become a critical factor in enhancing engine performance. As a core component of the thermal management system, the heat exchanger’s efficient heat transfer capability directly impacts the overall performance of the engine. In particular, under the increasing demand for compactness and high performance in modern aviation engines, researching novel high-efficiency heat exchanger structures and optimizing their design parameters holds significant engineering importance. Using computational fluid dynamics (CFD), this study conducted an in-depth analysis of different configurations of primary surface heat exchangers. Four distinct types of heat exchanger models were established: traditional rectangular (R) type, segmented rectangular (RS), cross corrugated tube (CC), and cross wavy (CW). A single-variable method was employed to systematically analyze critical parameters such as inlet temperature, flow velocity, and wall temperature. The results demonstrated that within the examined operating conditions, regardless of inlet variations, the flow distortion effect from corrugated tube structures significantly enhanced flow turbulence, thereby improving heat transfer performance while also introducing additional flow resistance. Consequently, CW-type heat exchangers exhibited superior heat transfer efficiency and flow resistance across all scenarios. However, in terms of comprehensive performance evaluation, CC-type heat exchangers achieved an optimal balance between heat transfer effectiveness and flow resistance. This research provided a detailed numerical analysis of internal flow and heat transfer characteristics for various heat exchanger types, offering theoretical support for the core optimization design of primary surface heat exchangers.