A vehicle body assembly system defines a preset pre-buck section and a preset main-buck section along a conveying route of a floor assembly, and may include: i) pre-buck units which are installed at both sides of the conveying route in the pre-buck section, respectively, restrict lower portions of side assemblies, which vary in accordance with a type of vehicle, with respect to both sides of the floor assembly, and preassemble the lower portions of the side assemblies to the floor assembly by a first welding robot; and ii) main-buck units which are installed at both sides of the conveying route in the main-buck section, respectively, restrict upper portions of the side assemblies preassembled by the pre-buck unit, and post-assemble vehicle body components to the upper portions of the side assemblies by a second welding robot.