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As the development of telecommunication technology, the cognitive radio is considered to be an effective way, and become the research focus in the past years. At the same time, the Auction Channel Allocation Mechanism for cognitive radio system which is validated is an effective and convenient way to solve the problem in cognitive radio. In this paper we discuss the problems encountered in the Auction mechanism of cognitive radio spectrum allocation, and explain the objectives pursued by the auction mechanism and the special problems encountered in cognitive radios. Finally, we propose an algorithm to solve the special problems and make simulations.