An encoding apparatus includes an intra-prediction module, a transform module and a control module. The intra-prediction module performs intra-prediction on an image block in a video frame according to a plurality of sets of reference image data to generate a residual block. The reference image data includes a set of reference image data corresponding to a predetermined side of the image block. The transform module performs preliminary transform on the residual block to generate a preliminary transform coefficient matrix. According to whether at least one of the reference image data corresponding to the predetermined side is generated according to image data of an adjacent pixel of the image block, the control module determines whether secondary transform perpendicular to the predetermined side is to be performed on a low-frequency component sub-matrix in the preliminary transform coefficient matrix.