Shanghai has attached great importance to science and technology in the economic and social reform. Shanghai has accumulated much experience and achievement in science and technology innovation. But there still exist some problems that obstacle science and technology development. The reason behind these problems is the defect of economic system and mechanism. In order to construct the science and technology innovation center which has great influence in the world，Shanghai should balance the relationship of government and market，leaving more room for the growth of market mechanism，which means further stimulating the vitality of enterprises，fostering the collaborative innovation，strengthening the coupling development of science，industry and social. Market should be the vital source of power that breaking down the system and mechanism obstacles. Enhancing the power of market，Shanghai should construct more open platform of science and service，promoting the innovation cooperation，giving all kinds of enterprises equal treatment，optimizing the system of talent evaluation and stimulation，adjusting the structure of its science and technology policy system.