The purpose of this paper is to analyze the factors affecting the emission of carbon compounds (carbon dioxide and carbon monoxide), resulting from energy consumption in the transport sector according to the subdivision (road, rail and air) for the period 1999-2011. For this purpose, index decomposition analysis (IDA) has been used. Factors influencing on carbon compounds emissions are coefficient of emission, energy intensity, changes in fuel mix, mode of transportation, structural changes, economic growth, population growth, and price. Results show that economic activity and population growth have respectively the greatest impacts on the on CO2 and CO emission in Iranian transport sector. The effect of coefficient of emission and changes in fuel mix varies during the years. The modes of transportation have little effect. Studying on price effects shows that low fuel price cause increase in carbon compounds emissions. The energy intensity and structural changes in the transport sector has been somewhat decreasing effect on emissions. In the road transport sector the situation is similar. In this section, the greatest impact coefficients of emission and changes in fuel mix have been on reducing emissions of carbon monoxide. In the rail and air sector as subsector transportation, scale of economic activity have greatest impact on CO2 and CO emission growth. The results show that the combined use of clean fuels, development of public transport and rail and infrastructure development in all sectors of transport can reduce emissions of carbon compounds.