We quantitatively analyze the relationship between China’s energy consumption, energy efficiency and economic cycle from the perspective of periodic fluctuations. Through HP filter analysis, the following main conclusions are drawn: First, the relationship between China’s energy consumption and output is nonlinear. Second, before the reform and opening-up, China’s output-energy efficiency changed greatly. After the reform and opening-up, the long-term trend has become relatively stable, while in the short term, the output-energy efficiency is more likely influenced by fluctuation factors. Third, from 2002 to 2005, fluctuations led to the decrease of output-energy efficiency in such industries as agriculture, industry, manufacturing, transportation and warehousing and the wholesale, retailing and lodging; and from 2010 to 2015, the overall output-energy efficiency was improved in such industries as agriculture, industry, manufacturing and the wholesale, retailing and lodging, mainly contributed by the trend factor. Based on these findings, we believe that long-term and short-term factors must be sorted out when preparing policy objectives and means for energy efficiency. From the perspective of sector-based analysis,the loss of energy efficiency is more attributed to short-term fluctuation factors, thus maintaining a stable economy is conducive to improving energy efficiency.