Reducing transportation carbon emissions in cities is crucial for sustainable development. Although polycentric urban morphology is viewed as a potential strategy for enhancing transportation carbon emission efficiency, its role remains contentious, and the effects of various dimensions of polycentricity have not been fully examined. This study investigates the spatiotemporal effects of polycentric urban morphology on transportation carbon emission efficiency. Analyzing per capita transportation carbon emissions (PTCEs) in 285 Chinese cities from 2000 to 2020, we quantified urban polycentricity across four dimensions: number of urban centers, distance between centers, sub-center importance, and compactness. We employed a geographically and temporally weighted regression model to assess how these dimensions influenced PTCEs over time and space. Our results reveal an overall increase in both PTCEs and polycentricity, with significant regional variations. Initially, the number of urban centers was negatively correlated with PTCEs, but this effect weakened over time. In contrast, greater distances between centers and higher compactness were associated with increased PTCEs, with these effects intensifying over time. The influence of sub-center importance on PTCEs followed an inverted U-shaped trend. Spatially, the number of centers correlated negatively with PTCEs, while sub-center importance correlated positively. The benefits of reduced distance between centers diminished from northeast to southwest China, and the impact of compactness on PTCEs varied, being positive in the east and negative in the west. These findings highlight the need for region-specific spatial policies to effectively enhance urban transportation carbon emission efficiency and develop low-carbon urban transportation systems.