In addition to direct thermal energy from a heating source, a large amount of thermal energy stored in clothing will continuously discharge to the skin after exposure. Therefore, thermal protective clothing may have a dual effect on human skin in reality. An experimental investigation was conducted to study the energy storage within 15 different combinations of clothing layers exposed to low heat fluxes ranging from 2.5 kW/m2 to 8.5 kW/m2. The energy storage process, the distribution of energy storage, and variables critically impacting energy storage, including fabric layers, air gap under clothing, thermal resistance and heat source intensity were discussed. It is demonstrated that the weight and thickness of the fabric are dominating factors affecting energy storage. For a multilayer fabric system, 36–57% of the total amount of energy is stored in the outer shell. The neighboring layer proves to be very important for the energy storage in an individual fabric. The air gap that exists between the fabric and the skin exerts an influence on the energy storage within fabric layers. In addition, a linear correlation is observed between the energy storage and the total thermal resistance of a fabric system. The research findings will be brought to researchers to better understand the mechanism and factors associated with energy storage and help develop new fabric combinations in order to minimize heat transmission to the skin.