The capillary microseparator is an important microfluidic device for achieving the inline separation of biphasic segmented flows. While it has found wide applications in areas such as on-chip synthesis of pharmaceuticals and fine chemicals, many aspects regarding its operating ranges and hydrodynamic details remain to be elucidated. In this work, we employ OpenFOAM computational fluid dynamics (CFD) method to systematically simulate the performance of the capillary microseparator under the retention, normal operation and breakthrough regimes. The three distinct operating regimes are in accordance with experimental observations. In addition, the simulations enable quantification of the instantaneous flow rate through each micron-scale capillary microchannel and provide detailed predictions even under very low pressure differences (∼10 Pa), both of which are difficult to achieve experimentally. Furthermore, inspired by high-resolution hydrodynamics from the CFD simulations, we develop a simple analytic expression that predicts the retention threshold of the microseparator in good agreement with the simulated results and recent computations and experimental data.