Urbanization and human activity have recently resulted in land use/cover change (LUCC), which has had a detrimental effect on the biological environment, on keeping the ecosystem’s sustainable growth and on comprehending the ecosystem’s quality and changes over the past 20 years in the central Yunnan urban agglomeration. The equivalent factor method and hotspot analysis were used to analyze the spatio-temporal changes in land use and ecosystem service value (ESV) in the urban agglomerations of central Yunnan province, and the effects of land use change on ESV were then examined. This study is based on the grid data of land use in 2000, 2005, 2010, 2015, and 2020. Finally, Geodetector was used to investigate the possible causes of ESV. The results showed that: (1) The urban agglomerations in central Yunnan’s land-use structure and pattern clearly changed between 2000 and 2020, with continual declines in grassland, cultivated land, and woodland, and constant increases in construction land. There was significant growth in both speed and area. (2) The average ESV of the land decreased consistently, the hotspot areas shrank, and the cold-spot areas grew as the ecosystem service function declined and the total amount of ESV decreased by 1.517 billion Yuan. These events were mostly explained by an increase in construction land and a decrease in grassland, cultivated land, and woodland. (3) The synergistic effect of numerous factors is what causes the change in ESV in the urban agglomerations of central Yunnan. The key forces behind ESV change in the research area were land-use intensity, normalized difference vegetation index (NDVI), slope, and people density. The results can help decision makers establish policies for ecological conservation and land use.