The estimation of inland waterway ship emission inventories through the Automated Information System (AIS) is associated with considerable uncertainty. A method for calculating the Inland Waterway Ship Emission Inventory Model (IWSEIM) was proposed, based on shipping material flow, to address this challenge. A comparison between CO2 emissions of inland ships calculated by the IWSEIM and the fuel consumption records revealed a relative error of 21.88%. The IWSEIM was applied to calculate the emission inventory of ships passing through a certain channel section on the Yangtze River channel during the whole voyage from 2017 to 2022. Cargo ships emerged as the primary CO2 emitters on the Yangtze River, accounting for 57.67%. CO2 emissions grew by 0.68% annually from 2017 to 2020. In 2018, SO2 and PM emissions decreased by 94.91% and 88.26% versus 2017. The emission intensity (g/t-cargo/km) of ships in the Yangtze River from 2017 to 2022 was calculated by integrating freight data and emission inventory results.