In laboratory systems engineering design, in addition to ensuring the scientific layout and state-of-the-art configuration of hardware facilities, special attention must be paid to establishing a robust safety management system. Safety is the paramount prerequisite for laboratory operations, encompassing multiple dimensions, including physical safety, chemical safety, biosafety, and information security. Accordingly, the design process should thoroughly account for the rational placement of emergency evacuation routes, the completeness of fire‑fighting equipment, strategies for the storage and disposal of hazardous materials, standards for the provision of personal protective equipment, as well as the compliant storage of biological samples and the proper handling of waste. At the same time, strengthening laboratory information management—ensuring the secure transmission and storage of experimental data and preventing information leaks—is an indispensable component. Furthermore, it is essential to establish comprehensive safety training and emergency response drill mechanisms to enhance laboratory personnel’s safety awareness and their ability to respond effectively to unforeseen incidents. In summary, laboratory systems engineering design must holistically integrate safety considerations, embedding safety principles into every stage of the design process, thereby fostering a research environment that is both efficient and secure for scientists and researchers.