•Total factor carbon emissions performance change for Chinese transportation sector is investigated.•The impact of regional heterogeneity is incorporated.•Metafrontier non-radial Luenberger carbon emission performance index is proposed.•Carbon emissions performance growth is mainly driven by technological innovation. This study examines and decomposes dynamic changes in total factor carbon emissions performance within the transportation sector in China, incorporating the impact of regional heterogeneity. For this purpose, we combine the metafrontier approach with the non-radial Luenberger productivity indicator to propose a new definition named the metafrontier non-radial Luenberger carbon emission performance index (MNLCPI). This total factor index includes the efficiency change, best-practice gap change, and metafrontier technology gap change indexes. This method is capable of measuring dynamic changes in total factor carbon emissions performance over time via the production frontier framework and can incorporate group heterogeneity and non-radial slack into its measurement of total factor carbon emission performance. Empirical results applying this method show a 6.2% increase in overall total factor carbon emissions performance for the 2000–2012 period. This growth in carbon emissions performance is mainly driven by technological innovation, and different growth patterns are observed across China’s three main areas in transport sector.