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Carbon dioxide (CO2), one of the major contributors to global warming and a factor affecting climate change, is predominantly emitted when fossil fuels are used to heat greenhouses during the winter season. Therefore, there is a need to implement adaptation of renewable energy to heat the greenhouses and reduce carbon emissions. In this study, the application of seasonal thermal energy storage (STES) using solar thermal energy (STE) sources in single and double-layered melon greenhouses was investigated with building energy simulation (BES). The double-layered greenhouse reduced the cumulative cooling load by 17.8% and the cumulative heating load by 61.6%, respectively, compared with the single-layered greenhouse, for which the cumulative cooling load was 42,714 MJ during the summer cropping season and the cumulative heating load was 36,531 MJ during the winter cropping season. Then, an STE-based STES system was developed and evaluated under various greenhouse conditions. When the STE-based STES system was applied to the melon greenhouse simulation, the required solar collector area and storage tank capacity for the double-layered greenhouse were 25-50% and 37-60% lower, respectively, than those required for the single-layered greenhouse. This study can contribute to the practical design of STES systems for melon greenhouses by providing a simulation-based method for estimating greenhouse heating demand and determining appropriate solar collector areas and storage tank capacities, thereby supporting sustainable agriculture by reducing fossil fuel consumption and mitigating greenhouse gas emissions.