Abstract: Sanitation is the key to preserving food and keeping food fresh. Aseptic packaging is paid more and more attention. In this paper, the structure of an aseptic packaging isolator was analyzed, and the conditions to ensure that there are no microbes in the aseptic isolator were studied. To ensure microbe obstructability of the three dimension turbulent flow field in the aseptic isolator, a new analysis method was used. Computational theory of three dimension turbulent flow field was analyzed, and then, the flow equations of the flow field were solved with Ansys Flotran Module. Through the appropriate theoretical calculation, the distribution of the flow field in the aseptic isolator was known entirely. The evaluation indexes of the microbe obstructability of the germ free isolator were established. The factors affecting these indexes were analyzed in detail. Considering microbe obstructability and economy, the reasonable structure and parameters of the germ free isolator were obtained. Mode one and mode two can meet the demand of microbe obstructability, we find that mode two is more reasonable. At the same time a vast amount of experimental data was obtained from corresponding model tests for verifying the computation, and a satisfying comparison was obtained.