The pebble bed high temperature reactors (PB-HTRs) are one of the promising reactor types for the next generation nuclear systems. Some intrinsic features of the PB-HTRs’ spherical fuel element embedded with the TRISO coated fuel particles bring high proliferation-resistance to the PB-HTR spent fuel storage, including the continuous on-line fueling strategy, the difficulty of processing TRISO particles, the low heavy metal density in the fuel pebbles and the high depletion of plutonium. The material accountancy concept and methodology of PB-HTR spent fuel storage are proposed in this work. For PB-HTRs, the spent fuel storage should be treated as an item facility; however, the items in PB-HTR spent fuel storage are the spent fuel containers, instead of the spent fuel assemblies in conventional PWR’s spent fuel storage. The accountancy of nuclear material should be implemented by evaluating the average burnup value of a batch of spent fuels. For the equilibrium core of PB-HTR, the average burnup value of a batch of spent fuel pebbles is determined by the integral power during the period when these pebbles are unloaded from the reactor core. Furthermore, the burnup value of each spent fuel pebble can also be measured by gamma spectroscopy upon the long-lived fission product 137Cs. After evaluating the spent fuel burnup, the dependency of the amounts of heavy metal nuclides upon the burnup value of a spent fuel pebble is estimated by the depletion calculations. It is revealed that the non-proliferation features of PB-HTR spent fuel storage is excellent and the accountancy methodology proposed in this work is feasible. Besides the high safety features, the high proliferation-resistance can be another attraction of the PB-HTRs.