Free trade zones represent an important system innovation space to realize economic agglomeration advantages with high-level openings. However, its evaluation of land intensive use has not received enough attention. The goal of this paper is to build a land use performance evaluation index system in line with the development trend of industrial economy and the characteristics of mixed land use in the free trade zones. An evaluation index system is constructed based on the three factors of land use status, land use efficiency and pilot free trade zone influence. Using the Delphi method and the entropy method, an empirical evaluation of the intensive land use level in the Shanghai Pilot Free Trade Zone is conducted. The results show the following: (1) integrating new indicators such as the free trade zone influence, social and ecological benefits into the evaluation index system show a characteristic and innovative land use evaluation; (2) in terms of the level of intensive land use, the Waigaoqiao Free Trade Zone has the highest intensity, followed by the Yangshan Free Trade Port Zone, and the Pudong Airport Comprehensive Free Trade Zone has the lowest intensity; and (3) development time, degree of land use, differences in leading functions, industrial land structures, and the diversification of employment structures are important factors that influence the differences in the levels of intensive land use in the Shanghai Pilot Free Trade Zone. This study also expands the performance evaluation of industrial land to the performance evaluation of construction land and provides references for industrial transformation and urban renewal of the Shanghai Pilot Free Trade Zone.