The use of micro/mini channels in heat exchangers can significantly enhance the heat transfer coefficient, reduce equipment size, and lower manufacturing costs. However, challenges such as manufacturing difficulties and scalability limitations remain. To address these issues, this paper proposes a novel assembly structure based on a honeycomb configuration, using modular cores, each containing a bundle of stainless steel tubes with an outer diameter of 3 mm and an inner diameter of 2 mm. A water-to-water heat transfer experiment system was established to investigate the heat transfer and flow resistance characteristics of the heat exchanger within the shell-side Reynolds number range of 200–1400. The results indicate that the prototype exhibits a shell-side heat transfer coefficient five times higher than that of conventional shell and tube heat exchangers, although the shell-side friction factor is correspondingly increased. The tube bundle structure was simplified using a porous media and dual-cell model, and CFD analysis was performed to investigate the mechanism through which the presence of blocking tubes enhances heat transfer performance. Furthermore, the causes of excessive shell-side resistance were analyzed, and an improved structure was designed to effectively reduce shell-side flow resistance. The design principles for this type of heat exchanger were proposed, providing a foundation for the further development of large-scale power heat exchangers.