A frame prediction system and a prediction method thereof. An initializing module initializes a first image block having a plurality of pixels. A providing module provides a first centroid and a first motion vector of a second image block. The location lookup module finds a location according to the first centroid, and generates a first weight and a second weight respectively according to a relationship between each of the pixels, the first centroid and the location. A vector lookup module finds a second motion vector, which gives a minimum pixel intensity error for the plurality of pixels in the first image block according to the first centroid, the first motion vector, the location, the first weight and the second weight. A processing module sequentially calculates a plurality of predictive intensity values according to the motion vectors and the weights.