Compared with the waste-to-heat and electricity-based hybrid refrigeration system, the innovative lab-scale refrigeration system integrated with the DC and AC cooling units that able to use solar and electricity as energy resources. Previous studies found that temperature control and uniform temperature distribution in refrigeration systems are both critical factors reducing vibrio growth on raw oysters and saving energy consumption. Therefore, this refrigeration system also equipped a specially designed divider and was used to test various air circulation strategies to achieve uniform temperature distribution in six individual compartments. The objective is to investigate and evaluate the effects of air circulation strategies and operating conditions on the cooling performance, including temperature distribution, standard deviation of compartment temperatures, and cooling time using a factorial design method. Results indicated the maximum temperature difference between the compartments was 8.9 ± 2.0 °C, 6.7 ± 2.0 °C, and 4.8 ± 2.0 °C in the scenarios of no air circulation, natural air circulation, and combined natural and forced air circulation, respectively. The interaction of fan location and fan direction showed a significant effect on the compartment temperatures while there was no significant effect on cooling time. A circulation fan on the lower part of the 12-volt section with an air supply from the 12- to 110-volt section was determined as the optimal condition to achieve relatively uniform temperature distribution. Refrigeration system also achieved a cooling temperature of 7.2 °C within 150 min to meet regulations. To that end, the innovative hybrid oyster refrigeration system will benefit oyster industries, as well as the aquaculture farmers in terms of complying with regulations and energy savings.