In order to improve the effectiveness of the judicial protection in our country, it is urgent to analyze the patent decision-making mode of the enterprise under the patent judicial protection system from the micro level, and to provide the policy guidance for adjusting the judicial protection of the patent. This paper first analyzes the general model of patent decision-making behavior under the patent judicial protection system, then makes an empirical study on the amount of patent infringement compensation in our country. Combining the empirical study results with the general model, the paper obtains the impact mechanism of patent judicial protection on patent decision - making behavior. Based on this, the paper analyzes the impact of the adjustment of the judicial protection system in our country on the patent decision-making behavior of the enterprise. The results show that the references factors for determination the statutory compensation in China covers the reference factors of determining the other three types of patent infringement compensation, and the statutory compensation has a certain positive effect. With the latest "Patent Law Draft Amendment (Draft)"the new patent law improving the statutory compensation and increasing the punitive damages, the patent protection will be obviously enhanced, then the enterprises are more inclined to choose the patent strategy of independent innovation.