In order to determine the optimal moulding process parameters of biomass seedling pots prepared from fermented cow dung mixed with corn stover, the moulding pressure, baking time, and baking temperature of biomass seedling pots were taken as the influencing factors, and the expansion rate, durability rate, wet swelling rate (48 h), and resistance to damage were taken as the evaluation indexes, and the Box–Behnken design of the response surface method was used to analyze the significance of interactions among the different influencing factors in the moulding process of biomass seedling pots and to optimize the moulding process. The experiment was conducted in the Biomass Laboratory of Heilongjiang Bayi Agricultural University. The response surface method Box–Behnken design was used to analyze the significance of the interaction between different influencing factors in the biomass seedling pots moulding process and optimize the moulding process. The results showed that the optimum moulding process conditions obtained using the Box–Behnken design were the following: a moulding pressure of 520.393 kN, baking temperature of 202.870 °C, and baking time of 8.573 min. The model was validated by testing and a response value of 10.522% was obtained for expansion, 99.598% for durability rate, 11.145% for wet swelling (48 h), and 4503.545 N for resistance to damage. The experimental verification showed that the deviation of the actual value obtained under this condition from the predicted value is less than 5%, indicating that the model reproduces well and meets the experimental requirements. Based on the optimal moulding process conditions determined in this experiment, the total porosity, EC, and pH of the Biomass seedling pots were determined to be 67.32%, 1.63 mS/cm, and 6.7, respectively, which met the seedling requirements.