Abstract: To analyze the coupling coordination development between innovation and urbanization of nine cities in Fujian, two evaluation index systems for urban innovation and urbanization were respectively constructed, and the comprehensive evaluation values were obtained from all index weights established by entropy method. The results showed that: (1) as a key breakthrough, the upgrading of the Industrial structure is essential for the economic transformation of Fujian; (2) as an important environmental support, the complete urban specialization function could create a favorable atmosphere for regional innovation development, and promote the coordinated development between urban innovation and urbanization; (3) as the interactive connection among cities, the traffic network should be extended in scope and more systematically designed in transportation ways, including constructions of highway, railway, etc.