Over the last decade, cyber-physical systems (CPSs) have seen significant applications in many safety-critical areas, such as autonomous automotive systems, automatic pilot avionics, wireless sensor networks, etc. A Cps uses networked embedded computers to monitor and control physical processes. The motivating example for this dissertation is the use of fault- tolerant routing protocol for a Network-on-Chip (NoC) architecture that connects electronic control units (Ecus) to regulate sensors and actuators in a vehicle. With a network allowing Ecus to communicate with each other, it is possible for them to share processing power to improve performance. In addition, networked Ecus enable flexible mapping to physical processes (e.g., sensors, actuators), which increases resilience to Ecu failures by reassigning physical processes to spare Ecus. For the on-chip routing protocol, the ability to tolerate network faults is important for hardware reconfiguration to maintain the normal operation of a system. Adding a fault-tolerance feature in a routing protocol, however, increases its design complexity, making it prone to many functional problems. Formal verification techniques are therefore needed to verify its correctness. This dissertation proposes a link-fault-tolerant, multiflit wormhole routing algorithm, and its formal modeling and verification using two different methodologies. An improvement upon the previously published fault-tolerant routing algorithm, a link-fault routing algorithm is proposed to relax the unrealistic node-fault assumptions of these algorithms, while avoiding deadlock conservatively by appropriately dropping network packets. This routing algorithm, together with its routing architecture, is then modeled in a process-algebra language LNT, and compositional verification techniques are used to verify its key functional properties. As a comparison, it is modeled using channel-level VHDL which is compiled to labeled Petri-nets (LPNs). Algorithms for a partial order reduction method on LPNs are given. An optimal result is obtained from heuristics that trace back on LPNs to find causally related enabled predecessor transitions. Key observations are made from the comparison between these two verification methodologies.