Biodiesel, as one of the most promising alternative fuels, has received more attention because of limited fossil fuels. A comparison of biodiesel and petroleum diesel fuel is discussed as regards engine unregulated exhaust emissions. A diesel fuel, a pure biodiesel fuel, and fuel with 20% V/V biodiesel blend ratio were tested without engine modification. The present study examines six typical unregulated emissions by Fourier transform infrared spectroscopy (FTIR) method: formaldehyde (HCHO), acetaldehyde (C2H4O), acetone (C3H6O), toluene (C7H8), sulfur dioxide (SO2), and carbon dioxide (CO2). The results show addition of biodiesel fuel increases the formaldehyde emission, and B20 fuel has little change, but the formaldehyde emission of pure biodiesel shows a clear trend of addition. Compared with the pure diesel fuel, the acetaldehyde of B20 fuel has a distinct decrease, and the acetaldehyde emission of pure biodiesel is lower than that of the pure diesel fuel at low and middle engine loads, but higher at high engine load. The acetone emission is very low, and increases for B20 and pure biodiesel fuels as compared to diesel fuel. Compared with the diesel fuel, the toluene and sulfur dioxide values of the engine show a distinct decrease with biodiesel blend ratio increasing. It is clear that the biodiesel could reduce aromatic compounds and emissions of diesel engines. The carbon dioxide emission of pure biodiesel has a little lower value than diesel, showing that the biodiesel benefits control of greenhouse gas.