Abstract: Throughout contemporary bioethics, environmental ethics, ecological ethics and medical ethics, the opposition between the concepts of naturalness and autonomy is like a red line that runs through discussions of almost all topics in these fields. Different understandings of the importance of naturalness and autonomy not only determine the differences between biological conservatives, biological liberals, and transhumanism, as well as the determination of the path for generating ethical norms, but also affect the moral understanding of human nature, life extension, and genetic enhancement. Through these discussions, the inherent strong logical explanatory power and competitiveness of the autonomy principle are clearly presented. While the autonomy principle provides support for people to modify nature and the natural genetic basis of humans, the principles of non-harm and justice determine the limits of such modifications.