Strategic emerging industry is the support of low-carbon economy, and its innovational is integration innovation. By analyzing the characteristic and actuality of strategic emerging industry and the advantage of integration innovation, the model of strategic emerging industry integration innovation can be classified into externally-driven and internally-driven types. The typical organization patterns are enterprise technology alliance, government-industry-university-institute collaboration, etc. And summarized the successful case of integration innovation in “chang-zhu-tan” urban agglomeration.