Valley shrink deformation is a common physical and mechanical phenomenon during the reservoir operation of high arch dams. This phenomenon is particularly significant in the initial stages of impoundment and can severely impact the operational safety of the arch dam. This study focuses on the arch dam under construction in the upstream of the Lancang River. By considering the secondary structural planes F115 and F111 at the dam site, a numerical model of valley shrink deformation was established. The study investigates the characteristics of valley shrink deformation during the initial impoundment phase of the arch dam. The results show that during the impoundment process, the valley slopes on both sides of the reservoir shrink towards the center of the valley. The deformation on the right bank is greater than that on the left bank due to the influence of the F115 fault. When the elevation is lower than the exposure position of F115, the deformation on the right bank increases with elevation; when it is higher than this position, the deformation decreases. On the left bank, due to the influence of F111 and the seepage field, the deformation value increases first and then decreases with the increase in elevation. After the water level stabilizes, the deformation rate decreases and approaches zero. This research results provide a reference for addressing valley shrink deformation issues during the initial impoundment of the arch dam.