The objective of this study was to investigate the effect of vibration on critical pore structure parameters related to flow in porous beds. The discrete element method was used to simulate particle packing in porous beds of soybean subjected to vibration. The porous bed was simulated as an assembly of spherical particles with diameters randomly distributed between 5.5 mm and 7.5 mm. The simulated porous bed was subjected to vertical vibration at a fixed frequency of 15 Hz and multiple amplitudes from 0.5 to 4.0 mm, resulting in vibration intensities from 0.45g to 3.62g (g = gravitational acceleration). The location (coordinates) of each particle was tracked during vibration. Based on the simulated spatial arrangement of particles, critical flow-related parameters of the porous bed, including porosity, tortuosity, and pore throat width were calculated. It was found that vibration intensity of 1.81g resulted in the lowest porosity, whereas lower vibration intensity did not have enough energy to densify the bed and higher intensity produced less dense parking due to over-excitement. Local porosity fluctuated markedly during vibration, with a general trend of decrease as vibration progressed. Vibration noticeably affected the shape (tortuousness) of flow path. Tortuosity of the porous bed before vibration was higher (2 % to 9 %) than that after vibration. Vibration reduced the pore throat width by 18 % on average (from 3.3 mm before vibration to an average of 2.7 mm after vibration).