River change is closely related to oasis and desert evolvement, and therefore has been one of the focuses in the study of environmental change in arid regions in recent years. The Manas river runs through mountain, oasis and desert systems and is the largest river in the Junggar basin. Previously, many studies about the Manas river focused on changes in the runoff, but the evolution of its watercourse was neglected. This paper investigates the evolution of the lower reaches of the Manas river using interpretation of remote sensing images, field measurements and deposition analyses. The results showed that three migratory occurrences and directions could be identified in the lower reaches of the Manas river during the past 4 000 years. The lower reaches of the Manas river ran along the watercourse R1 4 000 years ago, migrated 6 km south to Xinzhuangzi and ran along watercourse R2 4 000-1 500 years ago, then changed its route again near Taipingqu and created the watercourse R3 1 500-500 years ago. The last migration of the Manas river occurred in the 16th century when the Manas river left its western watercourse and moved towards the north, near the Jiahezi reservoir, and flowed along the south side of the desert creating the watercourse R4 which is the current watercourse. As a whole, the spatial evolution of the lower reaches of the Manas river has experienced a migration from south-west to north-east. With this knowledge, this paper concludes that geology and tectonic movement are the main factors which have affected watercourse evolution, but the roles of climate and riverside's composition are not neglected. Finally, this paper forecasts that the Manas river will not move on a large scale in the future without preternatural tectonic movement and climate change.