The booming of waterway transport urged the efficient management of CO₂ emissions from China's waterway transport sector (WTS). The transport structure changes due to the introduction of more inland and coastal waterway transport since the 12^th Five Year Period pose new challenges for the carbon-reduction management of China's WTS. This paper investigates the effect of transport structure change on CO₂ emissions from the China's WTS by an index decomposition model, which incorporates the transport structure change factor and three other important factors related to transport production. An empirical study conducted on 17 major waterway transport regions in China from 2010 to 2016 shows that the waterway transport structure change performed as a negative driver for reducing CO₂ emissions. However, a scenario analysis confirmed that effective transport structure changes would facilitate reductions in CO₂ emissions from the WTS. Industrial development was the greatest driver for CO₂ emission increase, while energy intensity change was an important driver for mitigating CO₂ emissions. Regional disparities on the effect of waterway transport structure change and industrial development indicated the necessity of collaboration among 17 provincial regions on waterway transport management to mitigate CO₂ emissions.