Abstract: The paper uses the panel threshold regression model to explore the difference of impact of innovation human capital investment on performance under different threshold effects with intellectual property protection intensity of regional innovation system as the threshold variable based on the panel data of China's 23 provinces and cities from 2009 to 2013 year. Empirical study results show that there is significant three threshold effect between innovation human capital investment and the lag two period of patent license quantity, and the influence coefficient of the innovation human capital investment on patent license quantity is 0.483, 0.682, 0.592, when intellectual property protection intensity is in the interval of [0.184, 0.256], [0.256, 0.448] and more than 0.448 respectively. The promotion effect first increase and then decrease. And there is significant three threshold effect between innovation human capital investment and the lag three period of new product sales revenue, and the influence coefficient of the innovation human capital investment on new product sales revenue is 0.503, 0.318, 0.241 when intellectual property protection intensity is in the interval of less than 0.140, [0.140, 0.980], and more than 0.980 respectively. The promotion effect gradually decrease. On the basis of empirical research, put forward the measures to promote the promoting effect of human capital investment to innovation performance from three aspects of the improvement of talent mechanism, improvement of intellectual property protection intensity, and effective transformation of scientific research achievements.