Based on analysis about the concept of scientific development，the theoretical foundation，main principles to establish the evaluation index system for urban scientific development will be pointed out in this article，and there are four subsystems to constitute the evaluation index system including “Economic Prosperity”，“Social Harmony”，“Environmental Friendliness”，and “Urban Supporting Capacity”. With the systematic evaluation on the scientific development level of over 286 prefecture-level cities in China，there exists strong positive correlation between urban scientific development level and urban economic development level. In view of the overall national situation，the cities of eastern regions，particularly the urban agglomerations in the Yangtze River Delta，Pearl River Delta，Bohai Rim areas，are China’s most mature area of urban development currently，with higher urban scientific development index in general；in the central regions，the cities’ scientific development index is close to that of the northeast，with social development lagging behind，and weakness of “Urban Supporting Capacity”，lack of further development and sustainability；in Western Regions，the cities’ scientific development index is slightly lower，with extensive development mode，fragile ecological environment and lagged social undertakings.