To achieve the efficient topology generation of upper-layer network in hybrid wireless NoC with large system size, a method of topology generation and performance enhancement based on channel assignment optimization is proposed. The method is implemented under certain signal-to-interference plus noise ratio (SINR) and strict resource budget by establishing relevant models of power consumption and interference for hybrid wireless NoC. A communication protocol with low overhead based on weighted conflict graph and two-level wireless token arbitration mechanism is designed for hybrid WiNoC with large system size. The designed protocol could handle channel contention and reduce the waiting time to get access to a wireless channel effectively. It improves obviously the frequency channel utilization. The experimental simulation demonstrates that the resulting topology generated by channel assignment optimization outperforms the conventional counterparts in terms of achievable throughput, power efficiency and latency at the cost of little area overhead.