This paper, according to China's fast marine economy growth and innovation and combined with marine economy innovation theories in the world, establishes an evaluation index system of marine economy innovation development from innovation environment, input, output and performance, and scores the 11 provinces/cities in their marine economy innovation development during 2010 to 2016 through centralizing the logarithmic primary data, covariance-improved eigenvalues extraction, and entropy-weighting principal component. System clustering is used to classify its hierarchy and to calculate the whole Moran's I index. Spatial correlation of Moran scatter points suggests China's marine economy innovation development is geographically of large difference between the north and the south, and balanced in the central, with each province/city slowly rising and a shrinking regional variance.