As an emerging form of agriculture, urban facility agriculture is an important supplement to traditional agriculture and one of the ways to alleviate the urban food crisis, but it may generate a high carbon footprint. A comprehensive assessment of urban facility agriculture is a necessity for promoting its low-carbon development. In this study, the carbon footprint of urban facility agriculture under four different technological innovation models was simulated by life cycle assessment and a system dynamics model for a carbon footprint accounting without considering economic risk. Case 1, as the basic case, is Household farm facility agriculture. Case 2 is the introduction of vertical hydroponic technology based on Case 1, Case 3 is the introduction of distributed hybrid renewable energy micro-grid technology based on Case 2, and Case 4 is the introduction of automatic composting technology based on Case 3. These four cases demonstrate the gradual optimization of the food–energy–water–waste nexus in urban facility agriculture. This study further uses the system dynamics model for carbon reduction potential considering economic risk to simulate the diffusion (promotion) scale and carbon reduction potential of different technological innovations. Research results show that with the superposition of technologies, the carbon footprint per unit land area is gradually reduced, and the carbon footprint of Case 4 is the lowest at 4.78e+06 kg CO2eq. However, the gradual superposition of technologies will further limit the diffusion scale of technological innovation, thereby reducing the carbon reduction potential of technological innovation. In Chongming District, Shanghai, under theoretical circumstances, the carbon reduction potential of Case 4 is the highest at 1.6e+09 kg CO2eq, but the actual carbon reduction potential is only 1.8e+07 kg CO2eq due to excessive economic risks. By contrast, the actual carbon reduction potential of Case 2 is the highest with 9.6e+08 kg CO2eq. To fully achieve the carbon reduction potential of technology innovation, it is necessary to promote the scale diffusion of Urban facility agricultural technology innovation by raising the sales price of agricultural products and the grid connection price of renewable electricity.