The location choice of emerging industries has always been the focus of economic geography research. "Windows of Locational Opportunity" and "Regional Branching" have different understandings about the relationship between local knowledge base and location choice of emerging industries. This study distinguishes the concepts of innovation cluster and industrial cluster, and holds that innovation cluster is more conducive to focusing on the location selection of emerging industries. Then taking China's fuel cell industry as an example, this study focuses on the applicability of "regional industry bifurcation" theory in the formation of fuel cell innovation cluster. And this paper divides the knowledge base into analytical knowledge, synthetic knowledge and symbolic knowledge. This paper collects patent information, patent citation and cited information, academic papers information of 291 prefecture-level cities in China from 2000 to 2016. With the aid of ArcGIS and Stata software, this paper carries out a spatial pattern analysis and two-step panel system GMM regression analysis, and draws the following conclusions. (1) From the perspective of pattern, the development of fuel cell innovation cluster is mainly concentrated in developed provincial capital cities, and a few other major cities such as Dalian. In the process of innovation cluster development, path dependence is obvious. The correlation coefficient of innovation cluster index of 291 prefecture-level cities in 2000-2005 and 2011-2016 is as high as 0.904, showing significant strong correlation. (2) Local analytical, synthetic and symbolic repositories all have significant effects on the development of innovation clusters, and the lagged first-order term of innovation cluster index is significantly positive, which supports that the local knowledge base has a significant positive impact on the development of emerging industry innovation cluster, and becomes an important evidence to support "Regional Branching". (3) The formation of fuel cell industry innovation cluster is mainly carried out in the way of "Regional Branching". The advantages of developed cities on the knowledge base help them to occupy an advantage in the formation of fuel cell innovation cluster, which leads to the further accumulation of knowledge-based advantages. Therefore, the virtuous circle between knowledge base and innovation cluster is formed, and path dependence is significant. Among the top 20 cities in innovation cluster index, the number of municipalities (at provincial level) and provincial capitals account for 75%, almost all other cities are located in the eastern coastal areas, which shows that it is difficult to open the location opportunity window of ordinary cities.