The accuracy of China's energy statistics is of great concern because it contributes greatly to the uncertainties in estimates of global emissions. This study attempts to improve the understanding of uncertainties in China's energy statistics and evaluate their impacts on China's emissions during the period of 1990-2013. We employed the Multi-resolution Emission Inventory for China (MEIC) model to calculate China's emissions based on different official data sets of energy statistics using the same emission factors. We found that the apparent uncertainties (maximum discrepancy) in China's energy consumption increased from 2004 to 2012, reaching a maximum of 646Mtce (million tons of coal equivalent) in 2011 and that coal dominated these uncertainties. The discrepancies between the national and provincial energy statistics were reduced after the three economic censuses conducted during this period, and converging uncertainties were found in 2013. The emissions calculated from the provincial energy statistics are generally higher than those calculated from the national energy statistics, and the apparent uncertainty ratio (the ratio of the maximum discrepancy to the mean value) owing to energy uncertainties in 2012 took values of 30.0, 16.4, 7.7, 9.2 and 15.6%, for SO2, NOx, VOC, PM2.5 and CO2 emissions, respectively. SO2 emissions are most sensitive to energy uncertainties because of the high contributions from industrial coal combustion. The calculated emission trends are also greatly affected by energy uncertainties - from 1996 to 2012, CO2 and NOx emissions, respectively, increased by 191 and 197% according to the provincial energy statistics but by only 145 and 139% as determined from the original national energy statistics. The energy-induced emission uncertainties for some species such as SO2 and NOx are comparable to total uncertainties of emissions as estimated by previous studies, indicating variations in energy consumption could be an important source of China's emission uncertainties.