The current certification process related to sustainable aviation fuel (SAF) has some problems to be solved, such as high testing costs, high testing fuel consumption, and the lack of safety criteria. In this paper, we proposed a system safety-based SAF safety assessment method and also offered a certification process for engine system safety. With the system safety of the engine as the top-level objective, the proposed method upgrades the similarity check from the fuel level to the engine level in the certification process. Not only the Safety Critical Parameters (SCP) are defined in this method, but also the SCP boundary for aviation kerosene is also used as a safety criterion for determining the safety of the SAF at the engine level. The adoption of the fuel technical standard orders (TSO) certification mode furthered the innovative concept of sustainable fuels as a special component of aero-engines, leveraging the experience of aviation kerosene operations and reducing certification costs. The certification process we proposed is capable of improving certification efficiency, reducing testing costs, and unlocking the potential of fuel components while maintaining system safety levels.