Homogeneous Charge Compression Ignition (HCCI) combustion was studied as a means of reducing PM and NOx emission simultaneously while maintaining high thermal efficiency and lower fuel consumption. An innovative low cost dual injection strategy is developed to investigate HCCI-DI combustion. This study is focused on the effect of fuel properties and cetane number on HCCI-DI combustion to understand the combustion and emission behavior of a direct injection HCCI engine using double injection strategy with blends of n-heptane and isooctane as fuel. A comparison is also made to understand the behavior and benefits of HCCI-DI combustion over the conventional combustion system. All experiments were carried out at a constant speed of 1350 rev/min and at zero, 15% and 30% of the full load conditions to avoid high knock intensity for high cetane fuel which occurs beyond this operating load condition. The most important finding is that a two phase heat release pattern is observed for high cetane fuel. As the quantity of isooctane is increased, low temperature heat release part diminishes and peak HRR, peak PRR and SOC moves away from the TDC due to longer ignition delay. It is observed that cetane number plays a major role in controlling the combustion phasing and emission behavior of the HCCI-DI combustion engine. A significant improvement in NOX and smoke emissions are observed in HCCI combustion when compared with the conventional single injection combustion for all five blends of the fuel. It is observed that fuel with lower cetane number helps in reducing smoke and NOX emission due to higher ignition delay with a marginal penalty in HC and CO emissions from such HCCI-DI engines.