Abstract: Liquid nitrogen rapid freezing has been widely used in the food industry. However, the high quality of lychees is often required after freezing, due to the uneven flow distribution and low heat transfer efficiency. In this study, a dual-objective optimization was proposed for flow field control, according to heat flux and spatial temperature. Both nozzle configuration and parameters were also considered during optimization. (1) Gas–liquid two-phase coupling behavior was considered for the spatial configurations of nozzles, namely the surrounding fan distribution (RFM) and the upper and lower “S” distribution (ULSM). Flow field and thermal performance were improved to balance the dynamics between the gas and liquid phases in the spray system. A comparative analysis of the flow field was conducted on two configurations, and the conventional rectangular distribution using CFD numerical simulations. Thereby, the superiority of the structure was validated to examine distribution features of the flow field. (2) A three-factor, three-level orthogonal experiment was designed with nozzle distribution, spray angle, and fan rotational speed as design variables. Numerical simulations were conducted using the ANSYS Fluent platform. Distribution characteristics of the flow field and temperature field were obtained under parameter combinations, leading to a multidimensional parameter space. Furthermore, a grid search algorithm was employed for global optimization, where a weighted score of heat flux and spatial temperature uniformity served as the objective function. The parameter combinations were traversed and then screened to identify the optimal scheme. (3) The optimal combinations of parameters were determined under the three nozzle layouts as follows: conventional rectangular distribution (ω = 1 160 r/min, θ = 0°), surrounding fan distribution (ω = 841 r/min, θ = 90°), and upper-lower "S"-shaped distribution (ω = 1 200 r/min, θ = 0°). Three groups of optimal schemes were compared with the original model (conventional rectangular distribution, injection angle 45°, and fan speed 1 200 r/min). The results show that the spatial temperature of the optimal scheme decreased slightly compared to the conventional rectangular distribution. The rest of the schemes were better than the reference case in the two indicators of heat flux and spatial temperature uniformity. Furthermore, the surrounding fan distribution (ω = 841 r/min, θ = 90°) was identified as the global optimal scheme, according to an equally weighted score of heat flux and spatial temperature uniformity. Furthermore, the better performance was achieved in 42.87% of heat flux and 4.09% of spatial temperature uniformity, compared with the baseline. Field experiments were conducted to evaluate the optimization performance of the flow field using the fruit cracking rate and target temperature achievement rate. The simulated temperature field was in great agreement with the measured, with a coefficient of determination (R²) greater than 0.98. The fruit cracking rate decreased from 23.3% to 16.7% after optimization, while the target temperature achievement rate increased 13.3 percentage points. The numerical model and optimal scheme can provide a scientific reference for structural design and energy efficiency of rapid freezing equipment.