Abstract: The passive residual heat removal heat exchanger (PRHR HX) is a key component of the third-generation advanced pressurized water reactor (PWR) nuclear power plant’s passive safety systems. The PRHR HX has numerous heat transfer tubes with varying lengths and arrangements on the primary side, leading to different flow distributions and resistance characteristics. The secondary side experiences various physical processes, including natural convection, mixed convection, and boiling heat transfer, significantly impacting the heat exchanger’s natural circulation and residual heat removal capacity. Current numerical analysis methods for PRHR HX inadequately consider flow distribution and resistance characteristics on the primary side. A porous medium-pipe-level coupling calculation method was established, introducing a parallel C-shaped pipe-level flow distribution and resistance iterative solution model. A matching strategy for grid control volumes on both sides and physical field communication was proposed, and a mathematical-physical model suitable for natural circulation and two-phase boiling conditions was developed for the PRHR HX, enabling coupling analysis between the primary side’s pipe-level resolution physical field and the secondary side’s porous medium computational domain. Based on data from Japan’s ROSA test facility, program validation was conducted, comparing heat transfer amounts, primary side outlet temperatures, and temperature profiles under single-phase and two-phase conditions, with good agreement between calculated and experimental values. Flow distribution and resistance characteristics on the primary side under coupled conditions of the AP1000 reactor’s PRHR HX was explored. The variation of secondary side thermal stratification with different operational parameters was analyzed. Results indicate that when the total flow rate on the primary side increases, the proportion of frictional pressure drop in the total pressure drop increases, diminishing the gravitational pressure drop’s dominant role in flow distribution, leading to reduced flow distribution unevenness. Additionally, heat transfer at the upper section increases, enhancing natural convection, resulting in faster thermal stratification on the secondary side, though with a lower Strouhal number peak. When the primary side inlet temperature rises, heat transfer intensifies on both sides, increasing the density difference at the inlet and outlet of the heat transfer tubes, thereby enhancing the gravitational pressure drop’s role in flow distribution unevenness. Consequently, flow distribution unevenness increases, with significant increases in upper section heat transfer and faster thermal stratification formation, while natural convection does not significantly enhance, resulting in a higher Strouhal number peak. When the secondary side’s initial temperature rises, heat transfer decreases on both sides, reducing the density difference at the inlet and outlet of the heat transfer tubes, weakening the gravitational pressure drop’s dominant influence on flow distribution unevenness, though the impact is relatively small. Additionally, the theoretical maximum temperature gradient decreases, slightly weakening the lower section heat transfer and natural convection mixing effects, leading to faster thermal stratification formation with a higher Strouhal number peak. This study can provide a reference for the numerical simulation analysis and optimization design of PRHR HX.