In the process design of falling film evaporator, there are uncertainties in the design parameters and heat transfer model, which increases the difficulty of falling film evaporator design. Therefore, based on the Monte Carlo uncertainty method, the influence of the uncertainty of the parameters and the model in the three-effect falling film evaporator of dairy products on the design results is studied. The results showed that, compared with parameter uncertainty, the change of evaporator heat transfer performance caused by model uncertainty was more significant. By comprehensively considering the influence of parameter uncertainty and model uncertainty, a model ensembling method was proposed to reduce model uncertainty and improve model prediction reliability. The heat transfer area of the evaporator was selected based on different design probabilities, which provided a theoretical basis for the design and operation of the evaporator under different design conditions and different operating conditions.