The objective of the present study was to apply two methods developed in ecology, the cycling index and input-output environs, to interpret nutrient flows in mixed rice-beef production systems. The cycling index (CI) was a quantitative measure of nutrient cycling. It was defined as the proportion of cycled nutrients to the total amount of nutrient flows. On the other hand, the input-output environs provide a quantitative distribution on a particular input or output. In this study, these methods were applied to the nutrient flows in the mixed rice-beef production systems in Japan. The results of CI provided information on the effects of nutrient cycling on the efficient conversion of nutrient imports to nutrient export. The results of input-output environs indicated that the indices represent indirect effects provided by the interaction between rice and beef production. In conclusion, these methods indicated new findings on nutrient utilization in the systems. The results of this study implied the further applicability of these two methods to the study of nutrient flows in mixed crop-animal production systems.