This study comprehensively evaluates thorium-based fuel utilisation in the Molten Salt Reactor (MSR) with a once-through fuel cycle. It examines the whether the use of thorium is beneficial in extending the fuel cycle length of an MSR, fuel utilisation efficiency, reactor safety, and reduction of long-lived radioactive waste. To observe those parameters, this research compares the use of thorium and uranium as fertile fuel in a single-fluid, once through MSR using Uranium-233 (U-233), Uranium-235 (U-235), and Reactor Grade Plutonium (RGPu) as well as the fissile driver. MCNP radiation transport code with ENDF/B-VII.0 continuous neutron library was used to analyse the neutronic parameters and fuel burnup in a multi-refuelling scheme for a total burnup time of 8 years. The findings indicate that the utilisation of thorium in conjunction with U-233 and U-235 significantly enhances fuel consumption and improve reactor safety. Such benefits, however, did not appear in RGPu. Moreover, thorium effectively reduces the production of long-lived radioactive waste, a crucial issue in nuclear waste management. Considering technical and environmental aspects, this study offers novel insights into using thorium as a more sustainable nuclear alternative under a once through fuel cycle, within a condition of multi-refuelling cycle which is only possible in an MSR.