We study the effect of the net toroidal plasma current on the diamagnetic measurement for large toroidal current experiments in the Large Helical Device (LHD). In order to treat precisely the effect, we apply a new method that evaluates magnetic fluxes of magnetic measurements directly from plasma currents of a magnetohydrodynamic equilibrium state with net toroidal current. There is a large difference between the value calibrated by the new method and by a conventional method under the cylindrical and large aspect ratio plasma model. We calibrate the diamagnetic beta value using the net toroidal current distribution observed by motional Stark effect spectroscopy in a LHD discharge with a high net toroidal current, 40 kA T−1. We obtain the results that the temporal behaviour of the calibrated diamagnetic beta value is quite the same with the beta value based on the profile measurement by Thomson scattering and far-infrared interferometry.