Since Wireless Sensor Networks (WSNs) are increasingly used in many industrial and civilian application areas, the correctness of their low level protocol such as the Flooding Time Synchronization Protocol (FTSP) is critical. However ensuring such correctness is difficult because of the complexity of the runtime environment. Model checking is an effective method for this problem, since it is a formal verification approach which has an advantage in exploring all behaviors of the system and discovering subtle errors. In this paper, we present a novel timed automaton model for FTSP. The main insight of our method is that by using timed automata, we can introduce the transmission delay and node failures that exist in real WSNs into our model and check whether FTSP is robust to node failures under a more realistic environment. We generate the timed automata models of FTSP and verify them by the model checking tool UPPAAL. Our evaluation result depicts an error of FTSP when the algorithm runs in the scenario that two root nodes fail continuously.