Objective To establish a method for determining reasonable control levels of chemical contaminants such as perchlorate in raw materials for infant formula by applying a probabilistic model. Methods Based on the levels of perchlorate in the raw materials of infant formula and the constituent ratio of ingredients, a probabilistic model between raw materials and final products was established using Monte Carlo simulation and the key influencing raw materials were identified through sensitivity analysis. The content threshold of perchlorate in the key raw material, which is the reasonable control level, was found by using step-back method according to the limit of perchlorate in infant formula. Results At the initial levels of perchlorate contamination in? raw milk,milk powder, lactose, whey protein powder and other ingredients collected in this study, the probability that the perchlorate level in the final product exceeds the limit value set by the European Union is 1.6% when a certain formula is used to manufacture infant formula. Sensitivity analysis shows that raw milk is the ingredient that has the greatest impact on the perchlorate content in the final product. Under the condition that the perchlorate in other raw materials remain the current level, if the probability of the perchlorate content in infant formula powder being lower than the limit value is expected to be above 99.9%, the perchlorate content in raw milk should be controlled below 43.6 μg/kg. When taking this value as the risk control level for perchlorate in raw milk, the current ratio of raw milk samples exceeding this level is approximately 3.5%. Conclusion The method established in this study can effectively simulate the probability distributions of stable chemical contaminants when transferring from raw materials to the final product and identify the most influential ingredient. By applying this method, the reasonable control level of perchlorate in raw materials of infant formula can be proposed, providing a scientific basis for infant formula enterprises to prevent and control risks of raw materials.