Separation membranes play a crucial role in the functioning of artificial organs, such as hemodialysis machines, membrane oxygenators, and artificial liver models. The current COVID-19 pandemic has highlighted the importance of these technologies in the medical community. However, membrane technology in artificial organs faces significant challenges, such as the clearance of low-middle-molecule and protein-bound toxins and limited blood compatibility. In this review, we will discuss the separation mechanisms, separation performance, and biocompatibility of different types of separation membranes used in artificial organs. We will also highlight the opportunities and challenges for next-generation membrane technology in this field, including the need for improved clearance of toxins and increased blood compatibility, as well as the potential for microfluidic devices.