Interannual and decadal scale changes in body size of Pacific saury, catch and catch per unit effort were examined to investigate the environmental effects on the stock structure and abundance in the Tsushima Warm Current region. Interannual changes in thermal conditions are responsible for the different occurrence (catch) rates of sized group of the fish. Changes in body size due to environmental variables lead the stock to be homogeneous during the period of high abundance, while one of the reminder cohorts supports the stock during the period of low level of abundance. Migration circuits of two cohorts of saury stock are hypothesized on the basis of short life span and spatio-temporal changes of the stock structure in normal environmental conditions. Changes in upper ocean structure and production cycles by the decadal scale climate changes lead changes in stock structure and recruitment, resulting in the fluctuation of saury abundance. Hypothesized mechanism of the effects of climate changes on stock structure and abundance is illustrated on the basis of changes in thermal regime and production cycle.