The innovation process is divided into two associated stages: technology R D and the development and sale of products. By using Two-stage DEA Model, correlated with shared input, to measure innovation efficiency, a comparative analysis of the gap is made between the innovation efficiency of seven high-tech zones in Fujian Province and nine advanced high-tech zones in China, where the meta-frontier model was used to overcome the problem of technological heterogeneity. The result shows that input excess and output deficiency of products are the common problems existing in these sixteen national high-tech zones. The efficiency of technology R D in seven high-tech zones in Fujian Province is generally low, and the overall innovation capacity is weak. Compared to the overall innovation capacity of nine domestic advanced high-tech zones, which is close to the innovation valid frontier, that of high-tech zones in Fujian Province is still in a quite big gap. The efficiency matrix shows that, except Xiamen high-tech zone, all the six high-tech zones in Fujian province are in a state of low technology R D efficiency and low product development and sales efficiency. Therefore, each national high-tech zone in Fujian Province should take active actions to explore the establishment of a third-generation science park, in which "Knowledge Innovation Community" acts as the core. In order to gain the leap in innovation ability, they should implement differentiation strategies to promote innovation capability, and make great efforts on both the research and development of technology and the development and sales of products.