A method and apparatus for controlling a backlight unit of a three-dimensional (3D) display apparatus receiving a 3D video sequence is provided. The method includes determining the image brightness level of the 3D video sequence displayed on a liquid crystal display (LCD) unit, for each of a plurality of partial regions of the LCD unit to which a plurality of sub-blocks of the backlight unit emit light; determining turn-on times of the plurality of sub-blocks of the backlight unit, based on the image brightness of each of the partial regions of the LCD unit; and determining turn-on periods of the plurality of sub-blocks of the backlight unit by synchronizing with a switching period between a set including a left visual point frame and a right visual point frame of the 3D video sequence.