In order to achieve the International Air Transport Association’s (IATA) goal of achieving net-zero emissions in the aviation industry by 2050, there has been a growing emphasis globally on the technological development and practical application of sustainable aviation fuels (SAFs). Discrepancies in feedstock and production processes result in differences in composition between SAFs and traditional aviation fuels, ultimately affecting the emission performance of the two types of fuel. This paper discusses the impact of CO2/NOx/SO2/CO/PM/UHC emissions from the aviation industry on the natural environment and human health by comparing the two types of fuel under the same conditions. Fuel combustion is a complex process in the combustor of an engine, which transfers chemical energy into heat energy. The completeness of combustion is related to the fuel properties, including spray, evaporation, and flammability. Therefore, engine performance is not only affected by fuel performance, but also interacts with engine structure and control laws. The CO2 emissions of SAFs differ significantly from traditional aviation fuels from a lifecycle analysis perspective, and most SAFs can reduce CO2 emissions by 41–89%. Compared with traditional aviation fuels, SAFs and blended fuels can significantly reduce SO2 and PM emissions. Pure Fischer–Tropsch hydroprocessed synthesized paraffinic kerosine (FT-SPK) can reduce SO2 and PM emissions by 92% and 70–95% respectively, owing to its extremely low sulfur and aromatic compound content. In contrast, the differences in NOx emissions between the two types of fuel are not significant, as their generation mechanisms largely stem from thermal drive and turbulent flow in the combustor, with emissions performance being correlated to power output and flame temperature profile in engine testing. CO and UHC emissions are related to engine operating conditions and the physical/chemical properties of the SAFs, with no significant upward or downward trend. Therefore, SAFs have significant advantages over conventional aviation fuels in terms of CO2, SO2, and PM emissions, and can effectively reduce the hazards of aviation to the environment and human health.