Inland shipping is pivotal to the comprehensive transport system of China. However, ship emission has become a major air polluter in inland river regions, and relevant emission inventories are urgently needed. Currently, the Automatic identification System based (AIS-based)emission model is widely used in calculating the ocean-going ship emission inventory. However, due to the lack of AIS data in the river area, the inland ship emission inventory mainly uses the fuel consumption method. With the continuous improvement of AIS data quality in the river area, the AIS-based emission model can be adopted in the development of inland ship emission inventory. However, there are few studies on the evaluation of the accuracy of the inland ship emissions using the AIS-based emission model. This study makes a comparison between test data and model-calculated data to evaluate the accuracy of the AIS-based emission models. Inland ship activities are divided into being at berth, maneuvering (port departure and port arrival), and on cruise modes in an AIS-based emission model. The model-calculated CO2, HC, and NOx emission rates can cover those onboard emission test data, but the values from the model are much lower. The total average ratios of test data to model-calculated data for CO2, CO, HC, and NOx are 2.66, 19.12, 2.46, and 3.16 when engine loads are below 60%. In upstream cruise mode, average emission rates of CO2, CO, HC, and NOx from the real-world test are 1.91–6.48, 8.78–27.83, 3.05–8.96, and 4.06–5.96 times higher than those from the AIS-based model, respectively. However, those are only 1.08–1.51, 6.74–9.67, 2.03–3.75, and 1.65–2.75 times higher than those from the AIS-based model in downstream cruise mode.