Border ports are the key nodes for economic cooperation among the sovereign countries at the Belt and Road Initiative. This study takes Manzhouli, the most closely connected port city on the Sino-Russian border, as an example. Firstly, by constructing the Modified Dynamic Concentration Index (MDCI), this study divided the process of the port-city relationship in Manzhouli into five stages: low level balanced development stage (1979-1987), port development slightly faster than the urban development stage (1988-1997), port development significantly faster than the city development stage (1998-2005), city development slightly faster than the port development stage (2006-2015), and new abrupt change point of port-city relationship (2016-2017). Secondly, the vector autoregressive model (VAR) is used to analyze the degree of influence at national, regional, local and individual scales on the Manzhouli port-city relationship. The research shows that in the whole period, the influence of different scales is manifested as national scale > individual scale > local scale > regional scale; at low level balanced development stage, the influence of national scale is larger, while that of regional, local and individual scales has less impact; at port development slightly faster than the urban development stage, with national scale as the main factor, the influence of Russia is slightly greater than that of China, and that of other scales is small; at port development significantly faster than the city development stage, all the national, regional and individual scales play an important role, and the role is relatively balanced; at city development slightly faster than the port development stage, the role of national, regional and local scales is more obvious, and the impact of individual scale is weakened. Among them, the regional scale has the largest impact, and the national scale (Russia) > local scale > national scale (China) > individual scale; at the new abrupt change point of port-city relationship, the influence of individual and national scales is larger, while that of regional and local scales is smaller. Finally, this study makes full use of both quantitative and qualitative analysis methods, such as VAR model and in-depth interview, to examine the influence mechanism of national, regional, local and individual scales on the evolution of port-city relationship in a full period and in stages. This study can provide a multi-scale perspective for Manzhouli to promote its benign development of port-city relationship, and also provide a reference for the development of port-city interaction in the vast border areas of China.