The invention relates to the technical field of construction building waste treatment, and discloses a vertical waste transportation system for a super high-rise building and a construction method thereof. Transport channels of the vertical waste transportation system are formed in a reserved space, penetrating in the up-down direction, on the inner side of the building, a supporting frame is arranged around the transport channels, and the transport channel in each floor is formed by connecting of a platform starting section and a plurality of standard sections; each platform starting sectionis arranged in a reserved hole of the last floor slab and is a circular-truncated-cone-shaped barrel with the large upper portion and the small lower portion and without a cover and a bottom, and a feeding inlet is formed in one side of the top end of each circular-truncated-cone-shaped barrel; and each standard section is a circular-truncated-cone-shaped barrel with the large upper portion and the small lower portion and without a cover and a bottom, the multiple standard sections are placed on the supporting frame in a lapped mode and comprise frame structures, horizontal supporting rods andhorizontal limiting rods, and the top end and the bottom end of each frame structure are fixedly connected with the lower surface of the last floor slab and the upper surface of the next floor slab correspondingly. The vertical waste transportation system is simple in structure, low in cost, convenient to use and wide in application range.