The fluctuation periods of annual energy ecological footprint (EEF) growth rate in China are analyzed based on empirical mode decomposition (EMD) method. The main factors which influence the per capita EEF fluctuation in China are discussed with factor analysis method, too. The results show that: (1) China per capita EEF kept increasing with fluctuation in the past 53 years. The obvious undulation cycles of per capita EEF growth rate in China are 4a, 13a, 17a and 27a over last 53 years. (2) The common influenced factors which correlative coefficients of EEF are prominent are founded at their different timescales. The first common influenced factors are growth rate of per capita GDP, growth rate of light industry production value, growth rate of secondary industry production value, growth rate of industry product value, growth rate of gross industrial output value, growth rate of total retail sales of consumer goods, growth rate of gross capital formation, growth rate of heavy industry production value, growth rate of tertiary industry production value, growth rate of construction production value, growth rate of transport, storage, post and telecommunication services. The analysis findings from the common synthesized factors of 4a, 13a and 17a timescales of the thirty-seven factors suggest that China′s energy policy-makers should attach more importance to stabilizing of economic growth, optimizing industrial structure, regulating domestic petroleum exploitation, and improving transportation efficiency, etc.