Nowadays, the increasing rate of human population in urban areas and the importance of urban functions pose a number of ecological cross-boundary challenges. The scientific research of the twentieth and twenty-first centuries revealed dramatic consequences of human intervention into natural ecosystems. The outcome of inadequate consumerism, which promotes industrial growth, and the pursuit of a better life is not only damaging to the natural ecosystems, but will eventually lead the World to dramatic climate change outcomes. Therefore, scientists are looking for ways for sustainable urban transformation without endangering the human population and the environment. According to the identified assumptions, the article investigates the principles of sustainable urban ecosystems. The authors consistently seek to explain the concept of sustainable urban ecosystems in both a broad and narrow sense, focusing on the individual constructs of this term—sustainability, city and ecosystems. The theories and approaches of urbanization and ecosystems are also analyzed in the article in order to highlight the opportunities and specific features of the application. The principles of sustainable urban ecosystems are provided in the modeled system which exposes the interfaces of identified principles and can be used for future studies.