The invention provides an alignment control system and method for glass deviation, and relates to the technical field of glass production. The system comprises a first driving shaft and a second driving shaft arranged above a conveying roller way and perpendicular to a conveying direction, a first photoelectric switch and a second photoelectric switch for detecting first edge points and second edge points of glass, a first control module for controlling the first driving shaft to move to the first edge points and calculating first displacement distances needed to correct the glass by the firstdriving shaft, a second control module for controlling the second driving shaft to move to the second edge points and calculating second displacement distances needed to correct the glass by the second driving shaft, and a lifting motor for hoisting the glass to correct the glass by the first driving shaft and the second driving shaft. The glass is corrected in a stop state, and the peripheral edges cannot be collided, so that the lower surface scratch and the edge scratch of the glass are effectively prevented when the deviation of the glass is effectively eliminated.