The comprehensive application of ecosystem service value (ESV) and ecological risk index (ERI) assessment can provide better decision support for regional ecological environment protection. Based on the remote sensing image data of Wuhu city of 1995, 2005 and 2016, the paper analyzed the spatial-temporal evolution of ESV and ERI in Wuhu city and its associated characteristics using an ESV, ERI assessments and a bivariate spatial autocorrelation method. The results showed that (1) the total ESV of Wuhu city continued to decline from 1995 to 2016, with a decrease of US$ 363.664 million. The total ESV per unit area of the sampling plot decreased, and the high-value was mainly distributed in areas within 5–10 km along the Yangtze River floodplain. (2) Wuhu city was mainly dominated by a relatively low ERI and medium ERI from 1995 to 2016. The high-value areas were mainly distributed in the mainstream of the Yangtze River, and the overall ERI improved. (3) There was a positive spatial correlation between the total ESV per unit area and ERI in Wuhu city, and these areas were mainly distributed in the Yangtze River mainstream region. According to this research, it is necessary to pay attention to the protection of wetland and forest landscapes, strengthen wetland ecological protection based on the Yangtze River and protect and restore natural mountain forests, all of which play important roles in improving the ecosystem service function of Wuhu city and protecting the ecological environment of the Yangtze River. We should act on that knowledge, and produce effective environmental regulations and habitat restoration efforts that improve the ESV and reduce the ERI. The findings of the study can serve as a reference for the management and protection of ecological environments in river-crossing cities.