This paper presents a temperature aware dynamic thread assignment scheme for a many-core processor. The proposed scheme uses a hardware based cluster controller to perform thermal management for each cluster of cores. The cluster controller performs dynamic thread assignment based on the thread transfer matrix with the following methods in descending priority: reducing the hot core temperature to closest to the threshold, transferring the fewest threads, and moving threads to the cores with the fewest active neighbors. The proposed scheme can achieve both good thermal management and high performance for processor cores.