In China, with the rapid development of economy and the advancement of urbanization, the deterioration of urban ecological environment is obvious. In order to obtain the quantitative state of urban ecological security, this paper contributes an integrated and coupled emergy ecological footprint framework and Beijing city was selected to verify methodology effect in this paper. The results demonstrate that: (1) from 2010 to 2019, the change range of EEFB is from 6.37 to 9.29%; meanwhile, EEFI is from 7.95 to 17.72%; EEFE is from 36.36 to 63.71%; EEFP is from 18.45% to 41.65%. Comparing the proportions of four subparts, the energy resource products (EEFE) and emissions (EEFP) are the main factors, far more significant than biological resources (EEFB) and industrial products (EEFI). (2) Compared to all ECCS data, there is a definite growing trend in Beijing city, from 2.68E + 4 hm2/cap in 2010 to 4.72E+4 hm2/cap in 2019, approximately 42.22% growth range. (3) Four sustainable indicators analysis: The changes of EEFT, EBI, and EEF are from 3.1, 2.46, and 1.02 in 2010 to 0.688, 9.29 and 1.14 in 2019, respectively. For EDI, total proportions of fossil land and built-up land are 85.25% to 90.43% of the entire EEF in Beijing city. These results reflect that Beijing city is suffering from a substantial ecological challenge due to remarkable ecological deficit, awfully high emergy ecological footprint intensity, and low cooperation level between ecological system and economic system. To identify key improvement factors, Pearson correlation analysis was conducted in this paper and revealed the most positive and negative elements, which are the unbalanced industrial structure and a large proportion heavy and polluting industries in Beijing city. Finally, based on the pivotal influencing factors, corresponding strategies and measures are proposed to improve and optimize the ecological security in Beijing city.