Abstract: Molten salt reactor (MSR), the unique liquid fuel reactor in the fourth generation nuclear power system, has great advantages in terms of inherent safety, neutron economy, nuclear non-proliferation, nuclear waste transmutation and thorium fuel breeding, compared with other solid fuel reactors. At present, there are two main types of molten salt reactor in domestic: Hexagonal assembly MSR and pebble-bed MSR. In this paper, the pebble-bed MSR fuel sphere homogenization method was studied with double heterogeneity characteristics taken into consideration, and the core fuel management code BORAGE was developed based on SIXTUS 3-D hexagonal node diffusion code. Numerical results suggest that the developed code achieves good accuracy, efficiency and can be used in MSR steady analytical calculation.