Build Quanzhou county economy innovation ability evaluation index system, collecting the relative statistic data of its 11 county economies from 2009 to 2014, the paper use SPSS software and apply principal component analysis methods to get the principal component scores and calculate the comprehensive score for the county economy innovation. According to the county innovation ability comprehensive score ranking and its static dynamic trend in the six years, Quanzhou counties are divided into three echelons, then analysis the innovation ability development characteristics of each echelon, the last part of the paper put forward the corresponding policy recommendations combined with the counties development characteristics.