Abstract: We find that eliminating molten salt and injecting poison into coolant both can be used as the auxiliary system of the second shutdown system in Pebble Bed Advanced High Temperature Reactor（PB-AHTR）. Compared with injecting poison into coolant, the effect of eliminating molten salt on the core is smaller and more beneficial to the engineering realization. Compared to one time charging scheme, batch charging scheme can ensure that the core excess reactivity is small in the whole life, which is more easy to control, but more complex to operate. In one time charging scheme, the second shutdown system gains enough fast shutdown margin by increasing the number of second control rod, not by reducing the stack height of core activity. A PB-AHTR core with burn up life of 100 equivalent full power days is proposed. Both the shutdown margins of the first shutdown system and the second shutdown system meet the design requirements.