The molecular mechanism of the microwave nonthermal effect is still not clear. This work investigated the spatial orientation and kinetic energy of active site collision of carnosine, a natural bioactive dipeptide, under the weak microwave irradiation using the molecular dynamics simulation. Our results showed the influences of the temperature, microwave intensity, microwave frequency, and microwave polarization mode (linear polarization and circular polarization) on the spatial orientation and kinetic energy of active site collision of carnosine. First, under the constant intensity and frequency of linear polarization microwave irradiation, the increment of the collision probability between the 6N atom of carnosine and the 28H atom of the other carnosine at effective space angle decreases from 85.0% to 3.5% with increasing temperature. Second, with the increase of microwave intensity, the change of spatial orientation and kinetic energy becomes more and more significant. However, the change of circular polarization microwaves on the spatial orientation and kinetic energy of collision is weaker than that of linear polarization. Third, under the constant intensity of linear polarization microwave irradiation, the collision probability between the 6N atom and the 28H atom at effective space angle decreases from 70.2% to 14.7% with increasing frequency. Finally, under the microwave polarization, the spatial orientation and kinetic energy of molecular collision are changed, which is summarized as the microwave postpolarization effect (MWPPE). The dependence of MWPPE on temperature, microwave intensity, microwave frequency, and polarization mode is very complicated. In the end, this effect can provide a new insight into the molecular mechanism of the microwave nonthermal effect.