In inertial confinement fusion, the sub-atmospheric purging through microcapillaries is of great importance to the high gas purity inside the cryogenic target and the low failure rate of experiments. In this study, a non-continuous flow model is developed for this sub-atmospheric purging process and verified through National Ignition Facility experiments to study the evolution of parameters such as pressure and gas composition that are not possible to measure directly. The effects of microcapillary structures and sizes on the transient evacuation–filling behaviors are analyzed, and the periodic purging scheme is optimized. The results show that the extension of evacuation and filling time caused by the elongated microtube can be described as a linear function of microtube length or an exponential decay function of microtube diameter, and the change of the inner diameter has a more drastic effect. The conical-straight composite can effectively reduce the evacuation and filling time while meeting the thermal and mechanical requirements. The overall performance of the purging process exhibits a strong dependence on the cycle trough pressure. The total purging time firstly decreases and then increases with the increase in the trough pressure, and the optimal trough pressure falls at around 20% of the filling pressure where the evacuation and filling times are almost evenly balanced. These results can provide theoretical guidance for the selection of microtubes and the design of the filling–evacuating scheme in the experiments.