As one of the candidate reactors for the fourth generation of advanced nuclear energy systems, High Temperature Gas-cooled Reactor (HTGR) has the inherent safety feature. The pebble bed HTGR adopts the fuel management mode of on-line continuous refueling, i.e., the refueling process along with power operation. The simplest way of refueling in the pebble bed HTGR is the once-through-then-out (OTTO) refueling scheme. While burnable poison particles need to be added to the fuel pebbles, in order to flatten the axial power distribution of the core. In this way, it is necessary to apply the fuel pebbles with higher enrichment to ensure sufficient reactivity in the core. However, the fuel utilization rate will be reduced, and there will still be considerable fissile nuclides in the spent fuel. The pebble bed HTGR can adopt the multi-pass refueling scheme to reduce the power peak factor, thereby reducing the amount of burnable poison particles and the enrichment of fuel pebble to cut the waste of fuel. The refueling speed will increase with the increase of the number of passes through the core, which brings more challenges to the fuel handling system. If multiple fuel handling systems are applied, the cost becomes higher. Therefore, the number of passes through the core should not be too high. Based on the equilibrium core of High Temperature Reactor—Pebble bed Modules (HTR-PM), the multi-pass refueling scheme with burnable poison particles added to the fuel pebbles is studied, aiming to flatten the axial power distribution of the core, control the fuel enrichment within an acceptable range and ensure proper refueling speed. This work has practical engineering value for the fuel management of the pebble bed HTGR.