In this paper, an eco-efficiency analysis is conducted using the epsilon-based measure data envelopment analysis (EBM-DEA) model for Russian cities along the Northern Sea Route (NSR). The EBM-DEA model includes five input variables: population, capital, public investment, water supply, and energy supply and four output variables: gross regional product (GRP), greenhouse gas (GHG) emissions, solid waste, and water pollution. The pattern of eco-efficiency of 28 Russian cities along the NSR is empirically analyzed based on the associated real data across the years from 2010 to 2019. The empirical results obtained from the analysis show that St. Petersburg, Provideniya, Nadym, N. Urengoy, and Noyabrsk are eco-efficient throughout the 10 years. The results also indicate that the cities along the central section of the NSR are generally more eco-efficient than those along other sections, and the cities with higher level of GRPs per capita have relatively higher eco-efficiency with a few exceptions. The study provides deeper insights into the causes of disparity in eco-efficiency, and gives further implications on eco-efficiency improvement strategies. The contributions of this study lie in the fact that new variables are taken into account and new modeling techniques are employed for the assessment of the eco-efficiency of the Russian cities.