Environmental and design factors determine the stormwater management capacity of green roofs; however, the design and environmental factors that impact their hydrological performance in subtropical humid regions are poorly understood. In particular, meteorological factors have received little attention. Meteorological factors vary greatly at different stages of a rainfall event (e.g., during the rainfall and outflow). Therefore, the impact of meteorological factors at different stages on hydrological performance should be considered separately to obtain a more accurate picture of their effects on hydrological performance. In this study, experimental green roofs were established based on four substrate types and two depths. For the first time, this study systematically explored the effects of design factors for the substrate (type and depth) and multi-stage environmental factors on the hydrological performance of green roofs. Environmental factors, including meteorological factors, from three critical stages (before and during a rainfall event and during the outflow), and rainfall characteristics (e.g., rainfall depth and rainfall duration) were incorporated to determine the variation in hydrological performance. The effects of multi-stage environmental factors on retention and peak reduction were analyzed, with a ranking of each factor’s relative importance. Environmental factors played a leading role in determining hydrological performance. However, the impact of multi-stage environmental factors was not as important as that of rainfall depth and antecedent volumetric water content. Differences in hydrological performance were compared across combinations of design factors. No significant differences were observed across substrate types and depths. However, potential interactive effects might exist, though these were not significant compared to environmental factors (e.g., rainfall depth and rainfall duration). These results confirmed that the meteorological factors in the different event-related stages significantly impacted the hydrological performance. Quantifying the effects of design and environmental factors is critical for hydrological performance evaluation. The results provided a broader perspective on understanding influence mechanisms of hydrological performance and highlighted the impact of microclimates on hydrological performance.