As a common means of building ventilation, monitor roofs have been employed to introduce indoor airflow via thermal buoyancy and/or wind. However, preventing rainwater from entering the room via the monitor roof has become an important practical issue. In this study, the effect of installing a rain shelter on the natural ventilation performance of a monitor roof was studied via computational fluid dynamics (CFD). The experimental monitor roof was 1.2 m in width and 1.2 m in height, with/without eave overhang. The results revealed that after rain shelter installation, a rain protection effect was achieved, and the ventilation rate increased because of flow structure conformity, with an overall average effectiveness of 1.02. The ventilation potential and the basic flow patterns corresponding to different design schemes were described in detail. Moreover, a correlation equation for the hybrid natural ventilation rate under the recommended design schemes was provided.