Spray auto-ignition experiments were carried out in a constant volume combustion chamber for some pure alkanes (n-paraffins with different chain length, cyclohexane, n-butyl cyclohexane, and isooctane) and blends of n-decane with Standard Blended Fuel (isooctane/n-heptane) and product gasoline. Test results showed that the reaction activity of n-paraffins was relatively high. Meanwhile, the auto-ignition characteristics differed significantly with the molecular structures of alkanes. Adding different volume fractions of n-decane to Standard Blended Fuel and product gasoline could improve the fuel reaction activity at varying degree. Finally, functional groups effects were used to simulate the relationship between the molecular topology and the auto-ignition quality.