Cities at Prefecture Level or above are very important in national economy and social development in China. In order to evaluate the comprehensive competitiveness level during multi-year of these cities, based on analysis of urban comprehensive competitiveness, grey clustering model and spatial analysis function of GIS are applied to analyze and evaluate the comprehensive competitiveness of 266 important cities during the 10th Five-Year plan (2001-2005). And from spatial scale, deeper study has been done for the spatial distribution mode of important cities in the whole country considering geographical, economical and social characteristics. The results show that by applying grey clustering model and method can solve the problem of comprehensive evaluation span several years, and provide an exercisable route to evaluating urban competitiveness multi-year comprehensively. There are distinct spatial characteristics of important cities of China in their regions. The research conclusions enrich the research contents of cities system in their spatial characteristics, and provide certain decision-making gist for comprehensive evaluation, spatial distribution, and development decision-making of cities.