Land use change (LUC) in trans-boundary watersheds is of great importance to environmental assessment. The Aksu River is the largest trans-boundary river crossing Kyrgyzstan and China, but there was little information on the LUC of the watershed. We quantitatively investigated the processes and trends of its LUC by using analytic models based on the land use data derived from the remote sensing images and topographic maps. The LUC was in the quasi-balanced status with a slight difference between the loss and the gain of the area for most land use types during the period of 1960-1990, whereas transferred to the unbalanced status with significant difference between the loss and gain of the area during the period of 1990-2008. At the same time, land conversion direction changed from two-way transition to one-way transition for the most land use types. The integrated rate of net change of land use during the period of 1990-2008 is 2.1 times of that during the period of 1960-1990. Information on the processes and trends of LUC is valuable for better understanding the environmental changes across the whole trans-boundary watershed, and helpful to decision-making management for Kyrgyzstan and China.