In this paper, the effects of intake temperature and methane energy ratio on emission and combustion phasing in reactivity controlled compression ignition (RCCI) engine have been numerically investigated. In this way, AVL-FIRE CFD code employing a detailed chemical kinetics mechanism is used for 3D simulation of combustion process and emissions prediction. Natural gas (NG) with higher octane number (ON) is mixed with air through intake port, while normal heptane with lower ON is directly injected into the combustion chamber during compression stroke. For validation, the results of RCCI engine have been compared to experimental data. For this purpose the effects of the premixed ratio (PR) of NG, normal heptane fraction, and intake temperature on several parameters such as in-cylinder temperature and pressure, rate of heat release, RI, ISFC, soot, and NOx are investigated. The results indicate that these parameters have significant effects on the heavy-duty RCCI engine performance and emissions. By increasing intake temperature the maximum of in-cylinder pressure, rate of heat release, and NOx emission increase significantly while soot emission decreases, also ringing intensity increases up to 10 %. On the other hand, increasing intake temperature reduces volumetric efficiency, as a result IMEP is reduced by 11%. Also by increasing methane energy ratio from 65% up to 85% in the constant intake temperature and pressure, the mixture ON will be risen, which would lead to an increases in ignition delay up to 5 crank angle. Consequently, IMEP as an important factor will be enhanced and also NOx emission decreases because of lower combustion temperature. Consideration of intake temperature and methane energy ratio show that these parameters can play an important role on controlling combustion phasing.