The Beijing-Hangzhou Grand Canal carries the multiple missions of cultural heritage inheritance, economic and social development and ecosystem protection, and the demonstration model of harmonious coexistence between human and nature. Exploring the internal relationship between ecosystem services and economic development and its changing rules can provide scientific support for the innovative and coordinated development of the Beijing-Hangzhou Grand Canal region in the new era. In this paper, the Jiangsu section of the Beijing-Hangzhou Grand Canal was taken as the research area, and the InVEST model, spearman correlation coefficient, coupling coordination degree model, obstacle degree model and contribution degree model were comprehensively used to describe the spatial and temporal distribution of ecosystem services and the dynamic change characteristics and laws of economic development level, and to explore the coupling and coordination relationship between ecosystem services and economic development and its contribution/obstacle factors. The results showed that: (1) There was significant spatial differentiation in ecosystem services within the Jiangsu section of the Grand Canal, with pronounced differences between the northern and southern regions. (2) The interannual variation of ecosystem service relationship in the Jiangsu section of the Beijing-Hangzhou Grand Canal was relatively stable. Except that the relationship between habitat quality and water conservation changed from a synergistic relationship to a trade-off relationship, the trade-off coefficient between other ecosystem services gradually decreased or the synergistic coefficient increased. (3) From 2001 to 2020, the economic development level and the comprehensive level of ecosystem services of each county in the Jiangsu section of the Beijing-Hangzhou Grand Canal did not change much, and gradually increased spatially from north to south, and the polarization was more serious. From 2001 to 2020, the coupling and coordination relationship between ecosystem services and economic development in the Jiangsu section of the Beijing-Hangzhou Grand Canal showed a gradual improvement trend, and the southern section was better than the northern section. (4) From the system layer, the average contribution degree of the economic development level and the comprehensive level of ecosystem services of the districts and counties in the Jiangsu section of the Beijing-Hangzhou Grand Canal to the coupling and coordination relationship between ecosystem services and economic development was 0.74 and 0.27, respectively, and the average obstacle degree was 0.69 and 0.31, respectively. From the indicator layer, the key contribution factors and obstacle factors of each district and county were different. Based on the results, policy recommendations are proposed to promote the coordinated development of ecosystem services and economic development.