During filling in 1992 of the Tongiiezi reservoir, in Southwest China, it was noticed that the dam body and the rock masses on the right side of the valley were uplifted up to 22.2 mm and 24.3 mm respectively. After reservoir filling in 1993, the uplift continued, but the rate decreased, and the measured maximum uplift increased from 22.2 mm to 27.5 mm in the dam body and from 24.3 mm to 28.9 mm in the rock masses from 1993 to 2004. Based on the geological features of the dam site and observed geomechanics data, a numerical method is used to evaluate the representative elementary volume (REV) and to identify the parameters related to the mechanical and hydraulic properties of the rock mass. Furthermore, a coupled hydro-mechanical model is presented to describe the uplift process. The simulated results agree well with those measured. In addition, the time-dependent deformation is studied in the laboratory and numerically. It is concluded that, with the specific hydrogeological conditions at the Tongjiezi dam site, hydro-mechanical coupling during and after the reservoir impoundment is the main factor contributing to the uplift, and the time-dependent deformation is due to the rheological behavior of rock masses under seepage pressure.