Because of the poor oxidation stability and the high NOx emissions, biodiesel fuel was redesigned by adding anti-oxidants. The oxidation stability and viscosity of the biodiesel have been measured and analyzed. The engine experiment was conducted and it was fueled by biodiesel and BHA/biodiesel, NOx emission and smoke were measured. The mechanism of anti-oxidants to decrease the smoke, NOx emission was discussed. The results showed that BHA additive was a high effective antioxidant of biodiesel, the viscosity of biodiesel was decreased slightly; and the emission smoke and NOx was decreased significantly, especially at the high load condition. Anti-oxidants can restrain the high-temperature dissociation of long-chain fatty acid molecules during the combustion process, and it can promote the quenching effects of free radical. Also, it can change the “trade-off” tradition relationship between smoke and NOx emissions. 