The appearance of a distant object, when viewed through a telephoto-lens, is often deformed nonuniformly by the influence of hot-air optical turbulence. The deformation is unsteady: an image sequence can include nonuniform movement of the object even if a stationary camera is used for a static object. This study proposes a multi-frame super-resolution reconstruction from such an image sequence. The process consists of the following three stages. In the first stage, an image frame without deformation is estimated from the sequence. However, there is little detailed information about the object. In the second stage, each frame in the sequence is aligned non-rigidly to the estimated image using a non-rigid deformation model. A stable non-rigid registration technique with a B-spline function is also proposed in this study for dealing with a textureless region. In the third stage, a multi-frame super-resolution reconstruction using the non-rigid deformation recovers the detailed information in the frame obtained in the first stage. Experiments using synthetic images demonstrate the accuracy and stability of the proposed non-rigid registration technique. Furthermore, experiments using real sequences underscore the effectiveness of the proposed process.