Uncovering the intricate relationships within the realm of ecosystem services (ESs) across various spatial and temporal dimensions, as well as their nonlinear relationships with natural-social factors, is a fundamental condition for regional ecosystem management. This study focuses on Honghe Prefecture, Yunnan Province, and it quantifies the supply of ESs at the grid and township scales, clarifies the interrelationships among ESs and influencing elements, and proposes cross-scale regional ecological management strategies. The findings indicate the following: (1) ESs exhibited spatial variability. In the last 20 years, the supply capacity of food production (FP) increased by about 46%, while other ESs showed a downward trend. (2) Synergistic effects among ESs primarily occurred between WY, habitat quality (HQ), carbon sequestration (CS), and soil conservation (SC), while trade-off effects mainly took place between FP and other ESs. (3) Significant and dramatic changes in the ecosystem service bundles were observed in the southern mountainous areas. At the grid scale, the overall area of the integrated ecological bundle declined by approximately 88%. However, the proportion of the HQ-CS key synergy bundle increased from 15.68% to 40.60%. Similar spatial patterns and trends were also observed at the township scale. (4) There was a notable reduction in the comprehensive supply of the ecosystem service index (ESI) in the southwest, in which human activities and climate drought factors played a major negative driving role, and some driving factors had threshold effects with the ESI. Existing research often ignores the nonlinear relationship between complex spatiotemporal dynamics and ecosystem services. Thus, this study constructed a comprehensive cognitive framework for regional ES status from the perspective of "supply-interaction-driving-threshold" for ESs, providing a more comprehensive understanding of regional ES management.