Growing and densifying cities set a challenge for preserving and enhancing green spaces to cool urban spaces. Green roofs, involving the planting of vegetation on rooftops, are regarded as an alternative approach to enhancing urban greenery and urban cooling. For better cooling performances, it is essential to reasonably configure green roofs, especially in real and complex neighborhoods. Therefore, the aim of this paper is to investigate the impact of morphological characteristics of green roofs on pedestrian cooling in real and complex neighborhoods. In specific, based on an ENVI-met model, we studied the effect of greening layout, coverage ratio, vegetation height, and building height on pedestrian air temperature reduction in the tropical city of Hangzhou, China. Results indicate green roofs could generate moderate effects on pedestrian air temperature reduction (around 0.10–0.30 °C), while achieving a cooling performance of 0.82 °C. Green roofs in upwind zones were able to generate the most favorable cooling performance, while green roofs in downwind zones made slight differences to pedestrian thermal environments. Green roofs with a low coverage ratio were not useful for lowering pedestrian temperature, and a greening coverage ratio of 25–75% in upwind zones was cost-effective in real neighborhoods. Locations that were horizontally close to green roofs enjoyed better cooling performances. Increasing vegetation height could strengthen cooling effects of green roofs, while an increase in building height weakened the cooling performance. Nevertheless, higher building height could enhance pedestrian cooling performances because of building shading effects. In addition, because of wind effects and building shading, building height limits for the cooling performance of green roofs could be higher than 60 m.