Regarding the high consumption of allium vegetables such as onion and green onion in the daily food basket of families, it is important to study the sustainability of their agricultural system. Thus, a thermodynamic analysis was carried out to assess the sustainability of the cultivation method management using an exergy-based approach. Onions and green onions were evaluated for mechanized cultivation and for traditional cultivation, respectively. The use of renewable energy in the cultivation system was proposed in the numerical method. The sustainability index and exergetic improvement potential were calculated. Moreover, and the improvement of CDP and RI factors was investigated based on the CExC approach. The results indicated energy consumption of 1 ton of onion production was 2.5 times that of green onion production. The human labor and electricity as energy-intensive inputs in the process of green onion and onion production, respectively. The GHG emission of 1 ton of onion production was obtained 3 times that of green onion production. The results showed that the impact of using the new strategy in the agricultural system of green onions is less than onions, due to the high human labor requirement in green onion production, which made the production of green onions even more unsustainable than the production of onions, despite less consumption energy in green onion production.