Recent Network on Chip (NoC) design must take the thermal issue into consideration due to its great impact on the network performance and reliability, especially for 3D NoC. In this work, we design a virtual channel based fully adaptive routing algorithm for the runtime 3D NoC thermal-aware management. To improve the network throughput and latency, we use two virtual channels for each horizontal direction and design a routing function which can not only avoid deadlock and livelock, but also ensure high adaptivity and routability in the throttled network. For path selection, we design a strategy that takes priority to the distance, but also considers path diversity and traffic state. For throttling information collection, instead of transmitting the topology information of the whole network, we use a 12 bits register to reserve the router state for one hop away, which saves the hardware cost largely and decreases the network latency. In the experiments, we test our proposed routing algorithm in different states with different sizes, and the proposed algorithm shows better network latency and throughput with low power compared with traditional algorithms.