Green roofs have gained relevance in urban sustainability and affect the urban food-water-energy nexus in cities in many different ways. However, it remains unknown regarding systemically quantifying the trade-offs of green roofs on urban food-water-energy nexus. Most city-scale research is restricted to a silo lens (e.g., life cycle impacts and food-water-energy related benefits) while research focusing on green roof’s multiple trade-offs occurs at smaller scales (e.g., neighborhood). Here we developed a generalizable integrated methodology framework for data-sparse cities to analyze the food-water-energy nexus of green roofs from an urban system perspective and tested the framework in two global south cities, São José dos Campos, Brazil and Johannesburg, South Africa. We find São José dos Campos could reach its total self-sufficiency of vegetables in prospect by green roof farming, whereas its life cycle energy consumption would achieve 45% of urban energy demand in the worst scenario. Fueled by the scheme of rainwater substitution, 96% of the life cycle water consumption in São José dos Campos rushed to the infrastructure stage from the operation stage. Johannesburg had potential to satisfy 73% of urban vegetable self-sufficiency and contribute 8% to the city’s alternative water supply goal by rainwater harvesting. Local food supplies are cardinal drivers of trans-boundary water footprints beyond the cities of both São José dos Campos and Johannesburg. We highlight the necessity to balance the trade-offs of green roofs orienting urban food-water-energy goals and call for opportunities for green roof practice in cities.