The coupled Atmospheric and Hydrological Modelling System (AHMS) combines a hydrological model (HMS) with the Weather Research and Forecast model (WRF) through the Noah-MP land surface scheme. This system is applied in offline mode to the hydrological processes in the Yellow River Basin which has been dramatically affected by intensive human activities over the past decades. In the earlier studies, the river water use for irrigation is often not considered, which is however an essential component of the water balance in the arid and semi-arid areas of the Yellow River Basin. Here, the channel routing model of the AHMS is extended to account for irrigation water taken from river. The irrigation water requirements are estimated based on the WATNEEDS model. AHMS is applied for the period 1979-2013 and the model results are compared with observations. It is found that for the upstream stations, the model simulated and observed streamflow are in good quantitative agreement. Comparison with the observed streamflow at the Huayuankou station near the outlet of the upper and the middle reaches of the Yellow River Basin shows that the model performance improves significantly with the consideration of irrigation. For the entire Yellow River Basin, the AHMS is found to perform well with consideration of irrigation water consumption. The progress achieved in the present work demonstrates the capacity of the AHMS for long-term hydrological simulations in the Yellow River Basin and the AHMS simulation provide a comprehensive and quantitative overview of the water resources in this important river basin.