The different carbonyl compounds emission from ethanol—biodiesel—diesel and diesel were investigated using high-performance liquid chromatography. The result showed that at rated speed, the overall specific emission of carbonyl compounds decreased by 2.98% at 10% load and 16.42% at 50% load, meanwhile, increased by 11.79% at full load. The C1~C3 pollutants of formaldehyde, acetaldehyde, acrolein-acetone are the main carbonyl compounds, and up to 91.9% among carbonyl compounds emission. In general, the emission of carbonay compounds decreased as load increasing or speed decreasing.