Ecosystem services (ES) are the foundation for the survival and development of human society. It is of great significance to clarify the trade-off and synergy between different types of ES in promoting regional sustainable development. This paper selects the western Jilin Province as a case, focusing on exploring the trade-offs and synergies of ES in ecologically fragile areas, enriching the geographical types of research on the relationships between ecosystem services. Utilizing the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model, this study focused on quantifying four pivotal services—carbon storage, water yield, soil conservation, and habitat quality index—over a two-decade span encompassing the years 2000, 2010, and 2020, and analyzed the trade-offs/synergies between the four ecosystem service functions. The results show that from 2000 to 2020, among the four ecosystem services, water yield and soil conservation increased by 13.57 × 109 m3 and 220.61 × 106 t, respectively, while carbon storage and habitat quality decreased by 5.09 × 106 milligrams and 0.01 units, respectively. At the regional scale, there were only synergistic relationships between carbon storage and soil conservation, and carbon storage and habitat quality. This study provides scientific references to promote sustainable development in the western Jilin Province and offers new insights into the trade-off and synergy of ecosystem services in ecologically fragile areas.