This work developed a computational fluid dynamics (CFD) model to analyze and optimize the design of a heat-not-burn tobacco (HnB) device, which is an electrically heated tobacco product. The associated mathematical models were derived to express the fluid flow and pyrolysis of tobacco porous media, which is assumed to follow Darcy’ law. In addition, an apparent kinetic model was implemented as a submodel to represent tobacco pyrolysis reactions. Simulation results of the CFD model were compared with experimental data for validation. The results elucidate the interplay between the heat transfer inside the tobacco substrate and the pyrolysis reactions. Case studies were conducted to reveal that the chemical components generated in the HnB are strongly affected by the temperature distribution inside, which can be controlled by the heater design and operation. This leads us to suggest a new design which has dual heat sources of a needle heater and a wall heater controlled at 468K. The proposed design is shown to increase the nicotine generation rate by 4.6 times while generating less amounts of harmful and potentially harmful constituents (HPHCs).