Abstract: There are three challenges needed to be solved in pebble bed-fluoride salt-cooled high temperature reactor (PB-FHR) by using the deterministic neutron analysis codes, which are homogenization of double heterogeneity fuel pebble, leakage effect during homogenization and the continuous movement of fuel pebble in the core and multi-pass fuel management mode. Based on DRAGON5 and DONJON5 codes, a PB-FHR fuel management code PBMSR was developed and verified. PBMSR was used to calculate the PB-FHR with different fuel cycle modes. The results show that the number of a fuel pebble passing the core has little impact on the optimal discharged burnup in the multi-pass fuel cycle mode, but has great impact on the axial power distribution.