The rising energy and sustainability challenges in post-harvest storage systems have accelerated the need of low-cost, energy-efficient cold storage. This study presents a comparative analysis of two-stage indirect-direct evaporative cooling (EC) system with conventional cold storage (CS) for preserving 25 tons of onions under hot and humid climatic conditions. A heat load-based design methodology was employed to develop the EC structure, incorporating sensible and latent heat calculations, product respiration, infiltration. Computational Fluid Dynamics analysis was performed to analyze air movement pattern and temperature distribu-tion inside onion storage structure. The design of EC was validated by the EvapCal software and experimental result. All the results are in good agreement with each other. The EC system, with a total investment cost of ₹3.36 lakh, has reduced heat load by 77.2% (from 102,000 BTU/hr to 23,328 BTU/hr) and daily energy consumption by 76.14% (from 150 kWh/day to 35.79 kWh/day), corresponding to a projected annual operational cost of ₹1.49 lakh, similar to CS but with much lower dependency on energy. The EC system also had higher air exchange rates (86 vs 40 ACPH) and lower spoiling rates (15 vs 25%). The EC technique showed 82% energy savings, increased shelf life and lower decay and sprouting rates in experimental experiments backed by CFD predicted airflow and temperature profiles. The EC approach offers a highly sustainable, low-cost solution suitable for small-scale farmers. The computational analysis confirms that EC systems offer energy-efficient alternative for hot and humid climate conditions.