Ecosystems are undergoing continuous degradation due to the dual perturbation of global climate change and human activities, posing unprecedented threats and challenges to the ecosystem services they provide. To gain a deeper understanding of the spatio-temporal evolution of ecosystem service value (ESV), it is essential to accurately capture the characteristics of its spatial and temporal changes and its influencing factors. However, traditional spatio-temporal statistical methods are limited to analyzing the heterogeneity of ESV in a single temporal or spatial dimension, which fails to meet the comprehensive analysis needs for spatio-temporal heterogeneity over an extended continuum. Therefore, this paper constructs a Bayesian spatio-temporal hierarchical model to analyze the ESV heterogeneity in both temporal and spatial dimensions in Northeast China from 2000 to 2020 to accurately identify the regions with unstable fluctuations in ESV and analyze the influencing factors behind them. It aims to comprehensively and systematically reveal the intrinsic laws of spatio-temporal evolution of ESV, and provide a scientific basis for relevant decision-making. The study found a continuous fluctuating downward trend of ESV in Northeast China from 2000 to 2020, with significant spatial and temporal heterogeneity. Notably, the distribution of hot and cold spots is regularly concentrated, especially in the transition zone from low hills to plains, which forms an “unstable zone” of spatial and temporal fluctuations of ESV. Natural factors such as NDVI and NPP exhibit a significant positive correlation with ESV, while social factors like population density and GDP show a strong negative correlation. Compared to traditional statistical methods, the Bayesian spatio-temporal hierarchical model, with its outstanding flexibility and accuracy, provides a new perspective and way of thinking for analyzing classical spatio-temporal problems. Firstly, the model examines time and space as a whole and fully accounts for the influence of spatio-temporal interactions on ESV. Secondly, the Bayesian spatio-temporal hierarchical model meets the needs of long-term continuous ESV outcome detection, which provides us with solid support for a deeper understanding of the evolution of ESV.