A pellet defect inspection system using a multi color tone control, which continuously transfers pellets to detect colors of the pellets, thereby determining whether the pellets are defective, and a method for controlling the same. The pellet defect inspection system includes: a pellet defect inspection device which includes a sorter to photograph a first surface (top) and a second surface (bottom) of each of the pellets while transferring the pellets to inspect the pellets so as to separate and remove pellets that are determined as defective and transfer and load non-defective pellets to designated positions; and a multi color tone pellet inspection controller configured to photograph the first surface and the second surface of each of the pellets transferred along a lane while controlling the pellet transfer and changing an RGBW irradiation section so as to analyze and determine an image.