The chemical composition of marketed gasoline varies depending on the crude oil, refinery processes of oil refineries, and season. The combustion characteristics of HCCI engines are very sensitive to the fuel composition, and a fuel standard for HCCI is needed for HCCI vehicles to be commercially viable. In this paper, the effects of the structure of the fuel components on auto-ignition characteristics and HCCI engine performance were investigated. The engine employed in the experiments is a research, single cylinder HCCI engine with a compression ratio of 14.7. The intake manifold was equipped with a heater attachment allowing control of the intake air temperature up to 150 °C at 2000 rpm. Thirteen kinds of hydrocarbons, 4 kinds of paraffins, 3kinds of naphthenes, and 6 kinds of aromatics, were chosen for the investigation, and 20vol% of each of the pure hydrocarbons was blended with the 80 vol% of PFR50 fuel. The HCCI engine was operated with the thirteen kinds of fuels under the same equivalence ratio, and the relative ignitability (the HI index: the hydrocarbon ignitability index, defined in this paper) of each hydrocarbon was calculated from the HTHR CA10 and evaluated. The parameters of the HCCI engine operations were the intake air temperature, engine speed, and intake oxygen content controlled by EGR. The test results show that the relative ignitability of the paraffins does not change with intake air temperature, engine speed, and intake oxygen content, but with naphthenes and aromatics there are changes by the intake air temperature and engine speed. As the intake air temperature increases, the relative ignitability of naphthenes deteriorates, while that of aromatics improves. With increasing engine speed, the relative ignitability of the naphthenes and aromatics deteriorates. To understand the ignitability of hydrocarbons, the relation between the hydrocarbon structure and research octane number was investigated. It is clearly shown that the ignitability differences of the hydrocarbons were mainly caused by the straight chain length of alkanes and side chains, the ring size of naphthenes, and the benzene ring in aromatics. Based on these findings, the HCCI engine test results were also statistically analyzed with the chemical structure parameters, and are discussed here. Further, the ignition timing of the HCCI combustion was estimated by the Livengood-Wu integral and compared with the engine test data.