Innovation is the core driving force for the high-quality development of China’s economy. As the main regional unit of the country’s participation in global competition，urban agglomeration should pay more attention to and grasp the trend of the times and promote regional development with innovation. The comparative analysis of the innovation efficiency and its influencing factors of the three major urban agglomerations in the eastern part of China is conducive to learning from each other，learning from each other，and improving together. Based on the panel data of scientific and technological innovation input and output of the three major urban agglomerations in the eastern part of China from 2013 to 2017，this paper uses the DEA model to measure the innovation efficiency of some cities in the three eastern cities，and compares the Beijing-Tianjin-Hebei urban agglomeration with the other two. The difference between the innovation efficiency of urban agglomerations and its influencing factors. The empirical results show that the innovation efficiency of the three major urban agglomerations in China is at a relatively high level. The innovation efficiency of the Pearl River Delta urban agglomeration and the Yangtze River Delta urban agglomeration is faster than that of the Beijing-Tianjin-Hebei urban agglomeration. Technological progress is the main source of innovation efficiency improvement. The factors affecting the innovation efficiency of large urban agglomerations are different. Government policies are the key factors affecting the innovation efficiency of Beijing-Tianjin-Hebei urban agglomeration. Talent reserve is the key factor affecting the innovation efficiency of the Pearl River Delta urban agglomeration. Manpower input，government policies，and talent reserves are all It is an important factor affecting the innovation efficiency of the Yangtze River Delta urban agglomeration.