The invention discloses a glass-less 3D video encryption method based on digital watermark encryption and a system. The method comprises steps that, step 1, randomized numbers are combined to form an original digital watermark in a random arrangement mode, and the original digital watermark is divided into m sub digital watermarks randomly; step 2, the m sub digital watermarks are respectively embedded in each viewpoint image of an two-dimensional frame image to acquire the watermark encryption two-dimensional frame image; step 3, step 1 and the step 2 are cycled till watermark encryption for all two-dimensional frame images is carried out, and the watermark encryption two-dimensional frame images are converted into glass-less 3D videos; and step 4, sub digital watermarks of viewpoint images included by glass-less 3D video frame images are extracted to acquire original digital watermarks. The method has properties of excellent robustness and invisibility, glass-less 3D videos can be rapidly and conveniently encrypted, copyright protection for the glass-less 3D videos can be further realized, and the video playing and displaying effects are not damaged.