Microwave nonthermal effect in chemical reactions is still an uncertain problem. In this work, we have studied the spatial orientation and kinetic energy of reactive site collision between benzyl chloride and piperidine molecules in substitution reaction under microwave irradiation using the molecular dynamics simulation. Our results showed that microwave polarization can change the spatial orientation of reactive site collision. Collision probability between the Cl atom of the C-Cl group of benzyl chloride and the H atom of the N-H group of piperidine increased by up to 33.5% at an effective spatial solid angle (θ, φ) of (100∼110°, 170∼190°) under microwave irradiation. Also, collision probability between the C atom of the C-Cl group of benzyl chloride and the N atom of the N-H group of piperidine also increased by up to 25.6% at an effective spatial solid angle (θ, φ) of (85∼95°, 170∼190°). Moreover, the kinetic energy of collision under microwave irradiation was also changed, that is, for the collision between the Cl atom of the C-Cl group and the H atom of the N-H group, the fraction of high-energy collision greater than 6.39 × 10-19 J increased by 45.9 times under microwave irradiation, and for the collision between the C atom of the C-Cl group and the N atom of the N-H group, the fraction of high-energy collision greater than 6.39 × 10-19 J also increased by 29.2 times. Through simulation, the reaction rate increased by 34.4∼50.3 times under microwave irradiation, which is close to the experimental increase of 46.3 times. In the end, spatial orientation and kinetic energy of molecular collision changed by microwave polarization are summarized as the microwave postpolarization effect. This effect provides a new insight into the physical mechanism of the microwave nonthermal effect.