In order to predict the regular temperature change in tuna during the freezing process for cold chain transportation, improve the quality of frozen tuna, and reduce the energy consumption of freezing equipment, a three-dimensional numerical model for freezing tuna of different sizes was established. An unsteady numerical simulation of the air velocity and flow field was combined with an analysis of the freezing process of tuna. This paper also studied the effect of air velocity, temperature, and tuna size on the freezing process. The numerical results show that there was a positive correlation between the cold source environment and the tuna-freezing process. Lower temperatures and higher air increased the velocity at which the tuna moved through the maximum ice crystal formation zone, maintaining a better aquatic product quality. In some cases, however, the smaller tuna models achieved a longer freezing time. Due to the difficulty of obtaining the whole tuna sample, the temperature curve and freezing rate over time obtained during the freezing process were tested using a tuna block of a specific size. The maximum error did not exceed 6.67%, verifying the authenticity and feasibility of the simulation.