Rapid urbanization in the Songhua River Basin (SRB), a crucial ecological barrier in China and Northeast Asia, has led to the degradation of ecosystem service functions and a decline in their value, thereby posing a significant threat to regional ecological security. Clarifying the complex coupling coordination relationship between urbanization and ecosystem services (ESs) and identifying the spatiotemporal heterogeneity of their interactions will facilitate the high-quality and coordinated development of urbanization and ESs in the SRB. This study employed a systems approach, treating urbanization and ESs as overarching systems and delineating different aspects of urbanization and ecosystem service functions as subsystems within these systems. The spatiotemporal characteristics of urbanization and the ecosystem service value (ESV) in the SRB from 1985 to 2021 were revealed. The coupling coordination relationship and the spatiotemporal heterogeneity of the interactions between urbanization and ESs in the SRB at both the system and subsystem levels were analyzed using the coupling coordination degree (CCD) model and the spatiotemporal geographically weighted regression (GTWR) model. The findings indicated that during the study period: (1) The urbanization index of SRB rose from 0.09 to 0.34, while the ESV experienced a decrease from 2091.42 × 107 CNY to 2002.44 × 107 CNY. (2) The coupling coordination degree (CCD) between urbanization and ESs in the SRB at both the system and subsystem levels increased significantly, generally transitioning from the moderately unbalanced to the basically balanced stage. Areas with high CCD values were mainly distributed in ecological function areas and low-level urbanized areas, while areas with low CCD values were mainly distributed in grassland ecological degradation areas, ecologically fragile areas, resource-dependent old industrial cities, and highly urbanized areas. (3) The subsystems of urbanization had an overall negative impact on Ess, with varying trends, but the spatial distribution pattern of the interactions remained relatively stable. Conversely, the subsystems of ESs all exhibited a trend of initially strengthening and then weakening their negative impacts on urbanization, and the spatial distribution pattern was highly correlated with the spatial distribution pattern of ESV in the SRB.