To investigate the effects of green roof retrofitting, the Tianfu Heyuan residential community in Fengxi New City was selected as the study area. A numerical model coupling hydrological and hydrodynamic processes was applied. Six rainfall return periods (1, 2, 5, 10, 20, and 30 years) were selected, along with five different green roof retrofit area scenarios, resulting in 30 retrofit conditions to examine the impact on runoff. The results show that green roof retrofitting can effectively mitigate surface waterlogging. When the rainfall return period remains constant and the retrofit area is maximized, the runoff control rate of green roofs can be increased by 11.09% to 16.20%, the peak flow reduction rate can reach 17.66% to 68.45%, the outlet peak flow reduction rate can increase to 17.49% to 37.40%, and the contribution rate of the green roof retrofitting can reach 14.20% to 16.77%. Meanwhile, the contribution rate at the outlet decreases as the retrofit area increases. When the retrofit area remains unchanged and the rainfall return period increases, both the green roof peak flow reduction rate and its contribution rate show a trend of first increasing and then decreasing, with the best effect observed at a 5-year return period, where the peak flow reduction rate can reach 68.45% and the contribution rate can reach 16.77%. The outlet peak flow reduction rate shows a trend of first decreasing, then increasing, and then decreasing again, with inflection points at the 5-year and 20-year return periods. The contribution rate at the outlet shows an overall increasing trend.