In view of the “innovation paradox” phenomenon that China’s sharp increase in patent is accompanied by the downturn in total factor productivity growth and the decline of economic growth rate, this paper empirically investigates the industrial structure threshold effect of patent structure on economic growth from the perspective of new structural economics, using China’s inter provincial panel data from 2002 to 2016. The results show that only when the patent structure adapts to the industrial structure can it promote economic growth, industrial development and total factor productivity. When the proportion of sales output value of labor-intensive industries to that of non-labor-intensive industries exceeds the threshold, that is, the industrial structure is more labor-intensive, non-invention patents representing imitation innovation are more conducive to economic growth than invention patents representing independent innovation. The innovation model suitable for regional economic development should match the stage and characteristics of regional industrial development.