The development of strategic emerging industries is a major national science and technology strategy,strategic emerging industry vertical integration of Patent Alliance on the industrial effects contribute to the development of regional industry. This paper constructs the strategic emerging industry vertical integration of patent alliance game model,analyzes the regional strategic emerging industry vertical integration of Patent Alliance on regional industry influence. Research found that regional strategic emerging industry vertical integration of Patent Alliance Construction Trend is instable,and is affected by existing regional industry patent alliance and regional resource endowment,vertical integration of Patent Alliance has a leading role in strategic emerging industry. Finally, this paper puts suggestions corresponding industry development.