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Efficient risk control is one of the key factors for the success of patent financing project. By using compound real option method, this paper studies the risk control of patent financing project from the angle of project design. The content includes risk analysis, the construction of compound real option and the evaluation of compound real option. The modified compound real option evaluation method is proposed. The improved method was applied in some project design and the order preference of plan is attained, and the ideal plan is ascertained.