Abstract: Use Artificial Neural Network and Ordinary Least Squares regression method to explore the effect of geographic proximity and cognitive proximity effects in the synthetic knowledge based and analytical knowledge based industry innovation in the national and the three regional levels. We find that geographical proximity effect on the synthetic knowledge based industrial innovation is significantly accelerated with the type of half inverted "U", and the influence degree is higher than the weak promotion effect of cognitive proximity. Geographical proximity effect on the analytical knowledge based industrial innovation is like narrow inverted "U", the influence degree is lower than the cognitive proximity effect. Geographical proximity effects are over saturated in the eastern region. Geographical proximity and cognitive proximity effects are positive in synthetic knowledge based industries but showing inverted "U" in analytical knowledge based industries in the central region. Cognitive proximity effects need to be more cultivated in both synthetic and analytical knowledge based industries in the western region.