Abstract: The Stochastic Finite Element Method,which is developed in structural dynamics,is introduced to be used in analyzing conduction heat transfer in foods with random variables of thermo-physical properties. The first order stochastic perturbation method and Monto Carlo simulation method are applied to analyze conduction heat transfer of foods in microwave processing. The results using the two different numerical methods are in high agreement, and the calculated efficiency of Stochastic Finite Element Method is much higher. The stochastic characteristics of food parameters and temperature distribution in microwave processing are illustrated and discussed.