Although much evidence about the helical tomotherapy system are available, there is not a document about the procedure of quality assurance (QA) for changing the beam model. This study establishes the commissioning procedure for modifying the beam model of helical tomotherapy. Firstly, some intensity-modulated radiotherapy (IMRT) plans were created, and compared them with the calculated dose and the measured dose. Secondly, the absorbed doses to water in the machine-specific reference field and the plan-class specific reference field with a protocol in Japan; Standard Dosimetry of Absorbed Dose to Water in External Beam Radiotherapy (Standard Dosimetry 12) were measured. Thirdly, we reconfirmed patient-specific quality assurance. The recommended commissioning procedure after the change of the beam model was shown through three verification processes. This report would be helpful for not only changing the beam model of helical tomotherapy but also introducing Standard Dosimetry 12 to a clinic.