A timing controller, a display apparatus, and an operation method thereof are provided. The display apparatus includes a display panel and a timing controller. The timing controller includes a refresh mark controller and a pixel controller. The refresh mark controller includes a refresh mark table, and a plurality of refresh marks in the refresh mark table correspond to a plurality of sub-regions of a display region in the display panel. The refresh mark controller determines whether the sub-regions need to be refreshed according to an image signal and responds to a specific sub-region required to be refreshed to adjust a specific refresh mark according to a mapping ratio. The pixel controller sequentially looks up whether the refresh marks in the refresh mark table are adjusted, obtains the sub-regions corresponding to the adjusted refresh marks according to the mapping ratio, and performs a pixel refresh operation to the sub-regions.