Abstract: To address the issue of poor freezing quality in lychees caused by uneven flow distribution and low heat transfer efficiency in existing liquid nitrogen quick-freezing machines, this study proposes a dual-objective optimization method for flow field control based on heat flux and spatial temperature uniformity, considering both nozzle arrangement and process parameter combinations. First, in consideration of the gas–liquid two-phase coupling effect, two novel spatial configurations of nozzle arrangements are proposed, namely the surrounding fan distribution (RFM) and the upper and lower “S” distribution (ULSM). These two configurations are devised to improve the flow field characteristics and thermal performance by leveraging the interactive dynamics between the gas and liquid phases within the spray system. Based on CFD numerical simulations, a comparative analysis of the flow field characteristics is conducted for the two innovative configurations and the conventional rectangular distribution configuration, thereby validating the distinctiveness and superiority of the novel structures in terms of flow field distribution features. Second, with nozzle distribution, spray angle, and fan rotational speed as design variables, a three-factor, three-level orthogonal experimental scheme is designed. Numerical simulations are carried out using ANSYS Fluent to obtain the distribution characteristics of the flow field and temperature field under different parameter combinations, thereby constructing a multidimensional parameter space. Furthermore, a grid search algorithm is employed for global optimization, with a weighted comprehensive score of heat flux and spatial temperature uniformity serving as the objective function, and the parameter combinations are traversed and screened to identify the optimal scheme. Finally, the optimal parameter combinations under the three nozzle layouts are determined as follows: conventional rectangular distribution (ω = 1160 r/min, θ = 0°), surrounding fan distribution (ω = 841 r/min, θ = 90°), and upper-lower "S"-shaped distribution (ω = 1200 r/min, θ = 0°). Based on the basic operating conditions of the original model (traditional rectangular distribution, injection Angle 45°, fan speed 1200 r/min), the above three groups of optimal schemes were simulated and compared. The results show that the spatial temperature uniformity of the optimal scheme with traditional rectangular distribution is slightly decreased, and the other schemes are better than the reference case in the two indicators of heat flux and spatial temperature uniformity. Furthermore, based on an equally weighted comprehensive score of heat flux and spatial temperature uniformity, the surrounding fan distribution (ω = 841 r/min, θ = 90°) is identified as the global optimal scheme. Compared with the baseline operating conditions, this scheme achieves a 42.87% increase in heat flux and a 4.09% improvement in spatial temperature uniformity. Finally, field experiments were conducted to evaluate the optimization performance of the flow field based on the fruit cracking rate and target temperature achievement rate. The results indicate that the simulated temperature field values are in great agreement with the measured data, with a coefficient of determination R² greater than 0.98. After optimization, the fruit cracking rate decreased from 23.3% to 16.7%, while the target temperature achievement rate increased from 80% to 93.3%. The findings verify the reliability of the numerical model and the effectiveness of the optimized scheme, providing a scientific reference for the structural design and energy efficiency improvement of quick-freezing equipment.