Internally enhanced surfaces such as micro-fins are an important class of heat transfer enhancement in commercial applications such as air conditioners and refrigerators. Normally, researchers follow a fixed procedure to generate macro correlations between heat transfer efficiency and micro-fins. The correlations only reveal how newly designed geometries affect the heat transfer and pressure drops but are not predictive for new geometries because the detailed flow physics are not identified. The goal of the paper was not to find a new Reynolds number-based correlation but to find flow structures responsible for the enhancement of heat transfer efficiency and understand the mechanisms behind the phenomena. The paper investigates how flow structures affect heat transfer, pressure drops, and temperature fields in the micro-finned duct. We utilized a large eddy simulation (LES) with a localized, dynamic kinetic energy, subgrid-scale model (LDKM) to predict turbulent flow structures. The numerical simulation includes both heat conduction in the metal structure and heat convection on the solid-fluid interface. The accuracy of the numerical model was verified by a telescopic particle-image velocimetry (PIV) system. Of special note was the strong match of PIV flow structures with numerical flow structures simulated with LES. Several problems about the relationships were discussed and solved.