Shell and tube heat exchangers are used to transfer thermal energy from one medium to another for regulating fluid temperatures in the processing and pasteurizing industries. Enhancement of a heat transfer rate is desired to maximize the energy efficiency of the shell and tube heat exchangers. In this research work, we performed computational fluid dynamics (CFD) simulations and experimental analysis on the shell and tube heat exchangers using round and hexagonal tubes for a range of flow velocities using both parallel flow and counter flow arrangements. In the present work, the rate of heat transfer, temperature drop, and heat transfer coefficient are computed using three turbulence models: the Spalart−Allmaras, the k-epsilon (RNG), and the k-omega shear stress transport (SST). We further utilized the logarithmic mean temperature difference (LMTD) method to compute the heat transfer and mass flow rates for both parallel and counter flow arrangements. Our results show that the rate of heat transfer is increased by introducing the hexagonal structure tubes, since it has better flow disruption as compared to the round tubes. We further validated our simulation results with experiments. For more accurate results, CFD is performed in counter and parallel flow and it is deduced that the rate of heat transfer directly depends upon the velocity of fluids and the number of turns of the tube.