Homogeneous charge compression ignition (HCCI) achieved by negative valve overlap (NVO) strategy can realize ignition phasing control through retaining residual gas. Except for the heating and dilution effects of residual gas, the presence of incomplete-oxidation products in residual gas also affects auto-ignition significantly. In order to investigate the compositions of incomplete-oxidation products, a fast instantaneous in-cylinder sampling system was developed. The in-cylinder sample gas was extracted just before the low temperature reaction and analyzed online quantitatively. It was found that the main incomplete-oxidation products in residual gas, which possibly have significant effects on auto-ignition, are short-chain hydrocarbons, aldehydes, and alcohols. Simulation analysis with a detailed chemical kinetic mechanism of gasoline surrogate was used to decouple the effects of these species. It indicated that CH2O, C2H4, and C2H2 play the most important roles in advancing auto-ignition. Also, the accumulation mechanisms of these main active species prior to auto-ignition are analyzed.