This paper has done some basic reseraches about the cluster analysis of Panel Datas,first introduces the basic method of cluster analysis ,then introduces the basic concept of Panel Data,and its basic classifies: Single index Panel Data and multi-index Panel Data ,and introduces the statistical description method of Panel Data ,discusses the cluster analysis of Single index Panel Data and multi-index Panel Data .Finally,making a cluster analysis of Shandong province 17 city multi index panel data towards its economic development ,the paper has analysed by factor analysis and calculated the comprehensive score of the 7 indicators to describe economic development ,building comprehensive evaluation matrix,turning the 3D multi index panel data into section Euclidean distance as the evaluation index to clustering the system,and has achieved good results, then puts forward some suggestions of regional coordination development for Shandong province.