Pebble bed reactors use cycling scheme of spherical fuel elements relying on fuel elements cycling system (FECS). The structure and control logic of FECS are very complex. Each control link has strict requirements on time and sequence. This increases the difficulties of description and analysis. In this paper, timed places control Petri nets (TPCPN) is applied for the modeling of FECS. On this basis the simulation of two important processes, namely uploading fuel elements into the core for the first time and emptying the core is finished by simulation software Arena. The results show that as TPCPN is able to describe different kinds of logic relationship and has time properties and control properties, it’s very suitable for the modeling and analysis of FECS.