Medical data security is an important guarantee for intelligent medical system. Medical video data can help doctors understand the patients’ condition. Medical video retargeting can greatly reduce the storage capacity of data on the premise of preserving the original content information as much as possible. The smaller volume of medical data can reduce the execution time of data encryption and threat detection algorithm and improve the performance of medical data security methods. The existing methods mainly focus on the temporal pixel relationship and foreground motion between adjacent frames, but these methods ignore the user’s attention to the video content and the impact of background movement on retargeting, resulting in serious deformation of important content and area. To solve the above problems, this paper proposes an innovative video retargeting method, which is based on visual attention and motion estimation. Firstly, the visual attention map is obtained from eye tracking data, by K-means clustering method and Euclidean distance factor equation. Secondly, the motion estimation map is generated from both the foreground and background displacements, which are calculated based on the feature points and salient object positions between adjacent frames. Then, the visual attention map, the motion estimation map, and gradient map are fused to the importance map. Finally, video retargeting is performed by mesh deformation based on the importance map. Experiment on open datasets shows that the proposed method can protect important area and has a better effect on salient object flutter suppression.