China has entered the economic transition in the post-financial crisis era, with unprecedented new features that significantly lead to a decline in its carbon emissions. However, regional disparity implies different trajectories in regional decarbonisation. Here, we construct multi-regional input–output tables (MRIO) for 2012 and 2015 and quantitatively evaluate the regional disparity in decarbonisation and the driving forces during 2012–2015. We found China’s consumption-based emissions peaked in 2013, largely driven by a peak in consumption-based emissions from developing regions. Declined intensity and industrial structures are determinants due to the economic transition. The rise of the Southwest and Central regions of China have become a new feature, driving up emissions embodied in trade and have reinforced the pattern of carbon flows in the post-financial crisis period. Export-related emissions have bounced up after years of decline, attributed to soaring export volume and export structure in the Southeast and North of the country. The disparity in developing regions has become the new feature in shaping China’s economy and decarbonisation.