Abstract: Innovation diffusion has an important and far-reaching impact on the adjustment and transformation of regional industry structure. Based on the method of agent-based simulation, through combining and integrating firm behavior in terms of technology innovation and diffusion at the micro-scale and global industrial structure optimization at the macro-scale, this paper conducts a new analytical framework used to further explore the impact of large sets of heterogeneous firms’ behavior on the evolution of regional industrial structure, and then examine the relationship between innovation diffusion and global industrial structure optimization. Results mainly show that as for China, process innovation is more beneficial to the rational development of industrial structure, and for USA, Japan and Russia, product innovation will be more effective. Moreover, compared to USA, China and Russia, increasing the product innovation scale is helpful for promoting industrial structure towards rationalization in these regions like India, Japan and EU. Furthermore, for these regions like China, Japan, India and EU, with the scale rising, process innovation is conductive to drive the evolution development of these regions’ industrial structure from the relatively inefficient primary industries to the relatively high-efficient secondary or tertiary industries, which would lead to the optimization and upgrading of their industry structure. However, as for USA and Russia, the moderate scale of process innovation would be more useful for them to promote industrial structure optimization. Additionally, research also suggests that the effect of the pattern of different innovation in a region is difference, and more importantly, there are also large differences among regional industry development impacted by the pattern of different innovation. Therefore, differential strategic choice of regional development driven by innovation should be paid more attention in regional economic governance. Also, there may be some matching between dimension of regional industry development and dimension of space of innovation, which could provide important theoretical basis for formulating some policies in terms of global economic governance.