A flat-pen automatic assembly line system includes a worktable, two sprockets, and an endless loop driving chain connecting the two sprockets. The two sprockets are mounted at the two ends of the worktable, respectively. A plurality of jigs on the driving chain receives pen barrels. A transporting rail supporting the driving chain is provided between the two sprockets. A pen-cap mounting station and a pen-cap pressing station are provided on the same worktable successively, and the pen-cap pressing station is provided with an automatic pen-cap pressing machine. The pen-cap mounting process and the pen-cap pressing process are completed on the same worktable and these two processes are linked via the same driving chain. Therefore, the assembly time is shortened and the assembly efficiency is improved. Furthermore, the pen-cap pressing process may employ an automatic pen-cap pressing machine. Therefore, labor can be reduced further, and assembly efficiency can be improved.