The dynamic behavior of groundwater flow has an important effect on the transportation of pollutants in the stratum. In this paper, we investigate the influences of inlet position, outlet position, and flow rates on groundwater flow behavior, using the pore-scale numerical simulation technology. It is found that the groundwater flow behavior in microstructure rock is heterogeneous and complex. The pore structure determines the local fluid flow behaviors. The flow velocity of the channels with dead end is relatively low. The velocity in the longitudinal channels is impacted by the transverse channels significantly. The magnitude of the inlet velocity has less effect on the fluid flow direction but more on the flow velocity. The inlet and outlet locations have significant effects on the fluid direction and velocity. This work investigates the groundwater flow behavior in pore channels affected by outlet and inlet positions and velocities, and quantitatively describes the flow behaviors in the time and location space at the pore scale.