<p>Top logistics enterprise plays an essential supporting role in the city’s sustainable development. According to the 2019–2021 list of China’s A-level logistics enterprises, this paper aims to explore the spatial heterogeneity of the factors influencing A-level logistics enterprises over time by using a multi-scale geographically weighted regression model. In addition, the spatial evolution characteristics of A-level logistics enterprises were analyzed through spatial visualization and density estimation methods. The results show that: (1) The spatial evolutionary pattern of A-level logistics enterprises in Chinese cities demonstrates simultaneous agglomeration-diffusion dynamics. (2) The MGWR model provides an innovative scientific approach to the study of spatial heterogeneity in logistics. Its regression results are more reliable. (3) Different factors have different scales and intensities of action in different periods and regions over time. In terms of time-series characteristics, the intensity and range of the influence of the 2021 significance indicators all expanded compared to 2019, with a fluctuating upward trend in the intensity of impact. At the same time, the variability in the intensity of the impact is more pronounced across cities. This study stresses the factors influencing the spatial heterogeneity of A-level logistics enterprises have different scales and intensities of action with cities over time and in different years, providing new insights for sustainable development of logistics enterprises and logistics location theory in heterogeneity research. By identifying key influencing factors, this study supports the planning of sustainable logistics enterprises.</p>