The loop seal connecting a steam generator and a reactor coolant pump has been shown to result in the early depression of core liquid level and the temporary heatup of fuel during a postulated loss-of-coolant accident for a typical pressurized water reactor. It is very crucial in the experimental and analytical domain to provide a comprehensive understanding of the physical phenomena occurring in the loop seal. A new approach is proposed to realistically simulate the flow behaviors occurring in the loop seal through the use of three-dimensional, first-principle equations and control-volume-based finite differencing methods. Several important phenomena can be reasonably captured by the current model, which includes the flow stratification, interface wavy phenomenon, initiation of a slug flow, oscillation of liquid in the horizontal pipe, and blowing out of the residual liquid. The trend of residual liquid level with the superficial velocity is predicted to reasonably match the test data Special attention on the problem of the loop seal is focused on the loop-seal clearing that is strongly associated with the temporary core depression. This phenomenon can also be simulated by the current model as demonstrated in the calculated results. The predicted threshold velocity agrees with the experimental data and the analytical results from appropriate correlations.