As with all other physical descriptions simulated by COMSOL Multiphysics, any description of heat transfer can be directly coupled to any other physical process. This is particularly relevant for systems based on chemical reactions and mass transfer along with fluid flow. These physics interfaces are found under the Heat Transfer branch ().

The basic functionality for simulating heat transfer in homogeneous media is described in The Heat Transfer Interfaces in the COMSOL Multiphysics Reference Manual.

The Fuel Cell & Electrolyzer Module has extra functionality for simulating heat transfer in porous media. The documentation of all features in The Heat Transfer in Porous Media Interface is found in the Heat Transfer Module User’s Guide, which is supplied with the Fuel Cell & Electrolyzer Module irrespectively of whether a separate Heat Transfer Module license is purchased.