The matrix models have been applied to evaluate the impacts and management of tree species. Modeling of invasive species using stage based matrix methods has not been exploited to understand the population structure of the invasive species. The study simulated using stage-structured Lefkovitch models to assess the population structure and impacts of invasive population growth within Mount Elgon Ecosystem. The survey data were used to calculate the transition probabilities and the growth rate (Kiptogot 𝜆1= 1.074 and Kimothon λ2 = 1.115 and Saboti λ3 = 1.118) in different forest blocks. These results indicate that Cestrum aurantiacum is increasing in population and could have effects on the population of other native species within ecosystems in the future.