Urban roof development serve as a form of urban tinkering that could provide favorable conditions to meet wicked food, water, and energy challenges. In this research, three urban roof systems are designed featuring food production, rainwater collection, building energy saving, and photovoltaic power generation, which are named the bare roof system, green roof system, and open-air farming roof system. Here we establish a generalizable framework to reveal the multifaceted tradeoffs of urban roof schemes integrating geographic information system, life cycle assessment, and multi-objective optimization and decision-making. Testing the framework in a typical compact city Shenzhen, China, results show that the rooftop suitability for food-water-energy function development within the city ranges from 26.21 % to 42.83 %. When implementing a city-wide roof system upscaling, the harvested rainwater on rooftops would contribute to 82.5 % of urban recycled water utilization target in 2035 and exhibit the fewest economic costs, but comes at the cost of life cycle carbon emissions and land occupation with 1850 kt and 140 km2. City-wide roof farming scenario shows potential to achieve the local self-sufficiency of vegetables, and stands out as the avoided transboundary energy footprints which are 4.5 times greater than life cycle energy consumption. Our research can foster the multiple tradeoff understanding between upscaling roof systems and urban food-water-energy nexus. The findings will assist in multi-objective decision-making for roof planning and sustainable transition in cities.