Abstract: As the electromagnetic environment is becoming more and more complex, the biological effects of electromagnetic radiation are getting more and more attention, especially electromagnetic non-thermal effects is still not fully understood. In this paper, the influence of microwave on the spatial orientation and kinetic energy of carnosine (bioactive molecule) collision was studied by molecular dynamics simulation method. The microwave post-polarization effect was proposed to illustrate the molecular dynamics mechanism of biological effects in electromagnetic environment. The results show that with the increase of microwave intensity, the total number of collisions with linear polarization increases by 2.9% to 13.3%, while the total number of collisions with circular polarization increases by 2.4% to 11.2%. In the range of specific spatial angles, the probability of collision with linear polarization microwave field increased by a maximum of 131.3%, and the probability of collision with circular polarization microwave field increased by a maximum of 47.1%. This study will help to reveal the molecular mechanism of the biological effects of electromagnetic environment.