By constructing the indicators of regional innovation concentration，we used several methods to do the analysis of spatial structure and temporal evolution trend of Guangzhou regional innovative output in 2005-2014. The results shows that there is a big difference in the overall innovation output and a certain degree of geographic concentration in the sub-regions of Guangzhou，however，the agglomeration of innovative output of Guangzhou was weakening，indicating strengthening of innovation competition and the trend of technology innovation spreading from innovation poles to the surrounding area in Guangzhou. By constructing a knowledge production function model and using GWR method，we studied the mechanisms of innovation output spatial distribution.