Abstract: Ecological modeling is an important part of ecological experiments. The modeling process can improve our understanding on complex system and our ability of system thinking. System dynamics is a methodology to describe and simulate complex systems with lots of feedbacks, which generally exist in ecology with biotic-abiotic interactions. Owing to its extraordinary features, systems dynamics software STELLA is widely applied in ecology and other disciplines. Systems dynamics and its modeling software STELLA was briefly introduced in this paper. Using STELLA software, three typical ecological models discrete population increasing model，ozone depletion model and population dynamic model of giant pandawere established to explain the applications of STELLA software in ecology.