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Innovation is the impetus and source of enterprise development, and the cooperatively technical innovation is become a main innovation method. It is necessary to take measure to prevent and indemnify the loss that the risk may bring. Because of the existence of the complex non-linear function mechanism between the risk factors, so the non-linear method can be used to research the keeping way and controlling mechanism of cooperatively technical innovation. At first, this paper analyzed the seeking method of enterprise cooperatively technical innovation risk, and the steps of seeking risks are presented. And then the concept of controlling risk regulation gradient is put forward, and the method of calculating risk regulation gradient is expatiated in detail. The nerve network is suitable for recognizing and simulating nonlinear system, and the wavelet transformation or the decomposition displays the good time frequency localization characteristic and the multi-criteria function, therefore the wavelet nerve network based on the wavelet decomposition and the nerve network has the good fault-tolerant ability and the non-linearity approaching performance. And based on this, a complete controlling risk model of cooperatively technical innovation is brought forward, and the algorithm of risk control model is discussed.