The microclimate environment can be conveniently controlled with accuracy by plant incubators, in which the cuttings propagation method can efficiently enhance seedling production. To ensure air flow evenly throughout the incubator, the scientific design of the air inlet is crucial. This study utilized a computational fluid dynamics (CFD) model to simulate the airflow patterns in a culture layer under different air inlet conditions. Furthermore, the optimal design parameters were determined by way of response surface methodology (RSM) and the Non-dominated Sorting Genetic Algorithm-II (NSGA-II). Adopting the optimal parameters, a prototype was manufactured, and a cuttings experiment was carried out with apple cuttings in the incubator. The results showed that the optimal air inlet radius is 90 mm, the optimal air inlet height is 188 mm, and the optimal uniform flow plate hole diameter is 13 mm. Meanwhile, the apple cuttings were able to root. Therefore, this incubator with optimal parameters can be used for cuttings. The study provides a methodological and theoretical basis for the future optimizing of air inlet parameters and promoting cuttings rooting.