Although aim of the environmental protection is conservation of ecosystem, there are only a few studies focusing on the effect of radiation on ecosystem. To understand the ecological effect of irradiation, microbial ecosystem, “microcosm”, which contains minimum components of ecosystem such as producer, consumer and decomposer, is useful because the natural ecosystem is too complex. The microcosm consists of three species, i.e. Euglena (producer), Tetrahymena (consumer), and E. coli (decomposer). The mathematical model and computer simulation model were also developed to understand the mechanism of ecological interaction using the results of acute exposure experiments of the microcosm, and we predicted Tetrahymena, which is the most radio-resistant among the constituent species, would be most sensitive in the chronically irradiated microcosm as a result of an indirect effect due to population decrease in E. coli. Recently we started chronic exposure experiments. The microcosms were irradiated with γ-rays at dose rate of 1.2Gy/day, 5Gy/day, 10Gy/day and 23Gy/day. From preliminary results, we found that the prediction from the models was different from the experimental results. Therefore, in this study, we improved our mathematical model and discuss the difference between the model and experiments.