Abstract: Purpose/Significance Pilot free trade zone is the forefront of the reform of Chengdu-Chongqing double-city economic circle. Analyzing the current situation of science and technology innovation policies and improving policy system of Sichuan and Chongqing Pilot Free Trade Zone to promote their technological innovation capability, helps Chengdu-Chongqing double-city economic circle into a “national influence of science and technology innovation center”. Design/Methodology This paper applies content analysis to establish a two-dimensional analysis framework “policy tools-scientific and technological innovation” based on the policy text, quantitatively compares the policy contents of Sichuan-Chongqing region with the first and second batches of pilot free trade zones (Shanghai Pilot Free Trade Zone, Guangdong Pilot Free Trade Zone e.g.) to find its deficiencies of the policies in the supply side, demand side and environment side. Conclusions/Findings The study finds that there are some shortcomings of science and technological innovation policies in the Sichuan and Chongqing Pilot Free Trade Zone: unbalanced uses of three policy tools, unreasonable proportion of various secondary policy tools, excessive uses of financial means, lacking long-term plans and so on. It should increase the use of environmental and demand-side policy tools, strengthen support for education and training, finance in technology, service outsourcing, and do a better job in supplementing the government’s work in public undertakings, target planning, regulation and trade supervision.