Disclosed are a glass panel packaging box and a de-packaging method thereof. The glass panel packaging box includes a box body and a cushioning separator plate arranged in the box body. The cushioning separator plate is arranged between two glass panels. The cushioning separator plate includes a main body corresponding to the glass panels and lugs respectively extending from two opposite side edges of the main body. The box body includes a bottom board and side boards perpendicularly connected to the bottom board. The side boards include receiving slots that correspond to the lugs. The glass panel packaging box and the de-packaging method thereof provide lugs on the cushioning separator plate to make separation of the cushioning separator plate and the glass panel easy so as to increase working efficiency and allow reduction of the thickness of the cushioning separator plate used with a large-sized glass panel.