The invention discloses a PUP (Percentage of Un-linked pixels) diagram based 3D image comfort quality evaluation system and method. The method comprises the steps of firstly introducing the concept of PUP; then mapping pixels to different feature groups by using directionality features and brightness distribution features of each pixel, performing feature classification, defining a specific calculation method for the PUP on the basis of feature classification, and reflecting the PUP of positive and negative parallax features through the definition of the specific calculation method for the PUP; determining three sizes of an image block according to a Percival comfort domain and a Panum fusion region by adopting a partial area overlapping image block extraction method, and generating PUP diagrams under different sizes; and finally extracting 3D image features through a positive and negative PUP mean value, a PUP front 5% mean value and a PUP rear 5% mean value, building a 3D image comfort model, and applying the 3D image comfort model to 3D image comfort quality evaluation. According to the invention, the concept of a PUP diagram is introduced, 3D image comfort quality evaluation is performed quickly and effectively without parallax calculation, and the effect is improved significantly.