The relationship and obstacles between sustainable development (SD) and ecosystem services (ESs) are crucial factors for SD decision-making and ecological conservation strategies. The production-living-ecological (PLE) functional perspective provides a new research entry point to analyze the interrelationship between the SD of human society and ESs. In view of this, based on the Sustainable Development Goals (SDGs), this study established an SD localization evaluation framework from the perspective of the PLE functions and subsequently evaluated the SD levels of 16 cities in Yunnan Province from 2005 to 2020. Furthermore, changes in the ecosystem service value (ESV) were explored by combining the PLE land classification and dynamic equivalence methods. The relationship between SD and ESV was then analyzed using the modified coupling coordination degree (CCD) model. Finally, the obstacle degree model was introduced to identify the main factors affecting the CCD level of the two systems. The results revealed the SD level in Yunnan Province to be high in the central region and low in other areas. From 2005 to 2020, the province’s SD level increased from 0.146 to 0.341. Furthermore, the main contribution of ESV originated from ecological land (over 90%). The ESV was higher in the southwest of Yunnan Province compared to that in the northeast. From 2005 to 2020, the ESV decreased by 2.231 billion CNY and was dominated by the regulation services. The CCD level increased significantly from 2005 to 2020. The CCD subcategory changed from SD lag to ESV lag and ESV-SD balanced type. Moreover, the dominant obstacle factors did not change significantly during the study period. The ESV and SD systems were dominated by regulation services and sustainable production subsystems, respectively. The research results have important guiding significance for further optimization of regional development strategies and ecological protection measures.