Rural electrification is constrained by grid extension infrastructural cost, isolated low rural populations, lack of anchor loads, and repayment potential of villagers while decentralized renewable energy power is constrained by high capital cost, low reliability, and non-workable business models. Solar thermal energy can produce electricity, heating, cooling, water, and fuel and has the potential for storage for livelihood applications. Hence solar thermal energy-based cogeneration and polygeneration systems have the potential for intervention in rural livelihoods with a focus on the energy-land–water-food nexus. However, standalone solar thermal systems are capital intensive and shadowed by photovoltaics. In the current work, an island in the Indian Ocean is considered for the study, and a solar thermal energy-based hybrid polygeneration system is designed with end products such as electricity, heating, cooling for food storage, and desalinating to get pure water. The turbine, VAM, pasteurization unit, and membrane distillation unit are the considered components in the present analysis. The thermodynamic properties of the key components of the polygeneration system are identified and the energy and entropy balance of the system is done. The levelised cost of production of polygeneration outputs for 25-year operational life with an accelerated depreciation of 30% of the capital cost, over 8 years is carried out. It is found that the electricity and water pricing are INR 14.71 and INR 14.01 per unit which are not attractive. Normalization is done by adjusting the price of other polygeneration outputs namely refrigeration, hot water, and pasteurizing to make the electricity and water pricing feasible to achieve an IRR of 12.99% and payback of 9 years at a 5% annual escalation. The social cost saved with the benefit of polygeneration outputs is cumulated considering value addition in the supply chain to save agricultural produce and milk, which otherwise would have spoiled. The annual carbon emissions that are curtailed with solar thermal polygeneration outputs are cumulated and found to be 434 tonnes of carbon. The social cost and environmental cost due to carbon are considered as an incentive in the cost economic economics of polygeneration system and it is found that the IRR and payback can be improved to 17.98% and 6.2 years respectively. The work recommends policy interventions to promote decentralized solar thermal polygeneration systems for impact on rural livelihoods with a focus on the energy-water-food nexus.