General declines in ecosystem service values (ESV) are acknowledged worldwide; however, rather few studies have quantitatively analyzed the interrelationship between changing rural settlements and values of ecosystem services. This study used the county of Tongyu in West Jilin Province, China, as a case study to analyze how changing rural settlements impact the values of ecosystem services on surrounding land in the eco-fragile areas during 1997–2010. Quantitative analytical techniques mainly include the buffer analysis and an ecosystem services valuation. The results show that as the area of rural settlements increased in 1997–2010, the structure of land ecosystems had changed significantly during this time period, causing a change in ESV that was observed with a decline by 1.87 billion yuan and above 20%. The degradation of grasslands, wetlands, and water areas, as well as the farmland reclamation, were the main drivers of the decreases in ESV. The effects of the increased rural settlements on the distribution and variation of ESV were larger than the decreased rural settlements, especially the new rural settlements whose effect was largest, and the effect of changing rural settlements on the values of ecosystem services on the surrounding land was significant in proximity to these settlements. In conclusion, the effects of rural settlement evolution on the natural environment were obvious in the eco-fragile areas. Thus the encroachment of rural settlements still requires enhanced supervision in land management practices, and the scale and spatial distribution of rural settlements should be befittingly allocated in the eco-fragile areas to reduce the disturbance to the ecosystem.