Today’s plant communities are the result of long-term interactions between vegetation and site factors including man-made impacts. Current species diversity reflects historical as well as environmental factors since environmental change and human activities lead to changes in species composition and competition through biological invasions. It means that biodiversity as an indicator for the well-being of ecosystems must consider the effects of invaders on an ecosystem. On the other hand, the existing methods for biodiversity index can not be used directly for cross-scale evaluation of vegetation. Hence, we proposed a 3-dimensional model derived from a logistic equation for calculating a combined index of native and non-native plant diversity for estimating ecosystem/environmental change. The two variables, based on the current and the theoretical maximum diversity of native and non-native plants on a given scale, and the result of the model are relative values without units and are therefore scale-independent. Hence, this model developed can be used directly for cross-scale evaluations of vegetation change, and for estimating ecosystem or environmental change over time.