This study develops and validates a transient three-dimensional computational fluid dynamics framework for the microclimate of photovoltaic-integrated green roofs. The model accounts for turbulence, radiation, shading, plant transpiration, and photovoltaic conversion. Comparisons of modeling choices show that transient simulations, a power-law inlet wind profile, and different heat-transfer representations for modules and vegetation better capture rooftop conditions. Under the simulated conditions, the green roof reduced roof and module temperatures by up to 13 °C and 1.6 °C, respectively, compared with a conventional rooftop photovoltaic system. The results identify sub-module convection as the dominant module-cooling pathway and provide guidance for system design.