The invention provides a system and a method for vertical alignment of a spent fuel transfer container and a horizontal storage module. The vertical alignment system includes a laser generator installed at a detection point above the horizontal storage module and at least two sets of laser detection devices. Each laser detection device includes a target device installed on a detection point abovethe transfer container, a laser sensor installed on the target device for detecting the laser emitted by the laser generator and passing through the target device and an alignment indicating unit connected with the laser sensor for turning on the power supply and issuing a prompt when the laser sensor detects the laser. When the alignment indicating units of the at least two sets of laser detection devices issue the prompt, the vertical alignment of the transfer container and the horizontal storage module is completed. Through the system and the method for the vertical alignment of the spent fuel transfer container and the horizontal storage module provided by the invention, the accuracy of the vertical alignment operation is improved while the work efficiency is improved and the irradiation dose to a staff is reduced.