Objective To establish a biological model with nanostructure and to investigate the characteristics of the thermal conduction by radio frequency electromagnetic radiation upon the model for the exploration of the possible mechanism of microwave non thermal effect. Methods The prepared nanogold labeled RNase S sample was analyzed by routine hydrolytic ability of poly c and CD spectroscopy. After confirmation of the successful recombination of the enzymatic structure and the recovery of the enzyme activity, thermal effects of RF on the sample, water and air were compared. Results The biological model designed and prepared by us satisfactorily simulated the native RNase A in both recovery of enzyme activity and conformation. Air sample in air bathing possessed an exponent decreasing function for thermal dispersion and an exponent increasing function for RF thermal effect. The redistilled water sample had a linear increasing function for RF thermal effect. Meanwhile, nanogold labeled RNase S in water bathing kept constant for RF thermal effect. Conclusion Micro eddy current local heating might occur in microstructure consisting of nanometal cluster. A biological macromolecule with nanostructure, acting as a source of thermal radiation and conduction, might resonantly interact with some changeable domains nearby, so the biological model keeps isothermal during RF heating. This may be a possible mechanism of nonthermal effect for microwave and other physical factors.