A vehicle body assembly system is provided. A pre-buck section and a main-buck section are formed along a transport path of a floor assembly of the system. In particular, the system includes a pre-buck unit disposed in the pre-buck section and that regulates a lower portion of a different side assembly for each vehicle model with respect to opposite sides of the floor assembly, regulates a cowl and a front roof rail with respect to an upper portion of the side assembly, and key-welds the upper portion of the side assembly, the cowl, and the front roof rail. A main-buck unit is disposed in the main-buck section and regulates a rear roof rail and a package tray with respect to the upper portion of the side assembly pre-assembled in the pre-buck unit, and key-welds the upper portion of the side assembly, the rear roof rail, and the package tray.