As the core of “Rise of Central China” strategy, the regional innovation capacity of the Wuhan Metropolitan Area is the key to enhance the innovation ability of central China and even China. High-tech industries are the key driving force to improving regional innovation. Studying the relationship between high-tech clusters and regional innovation capacity helps optimize the spatial layout of regional high-tech industries, upgrade the industrial structure and enhance regional innovation capacity. Based on the panel data of nine cities in the Wuhan Metropolitan Area from 2010–2019, we measure the regional innovation capacity and the degree of high-tech cluster using the super-SBM and locational quotient. Furthermore, we explore the high-tech cluster’s influence on regional innovation capacity by constructing a non-linear panel threshold model and a spatial econometric model. The results showed: 1) The innovation capability of the Wuhan Metropolitan Area shows a “W” type fluctuation upward trend, and the degree of the high-tech cluster is below the quotient level of 1, showing a continuous “M” type trend; 2) There is a non-linear double-threshold effect between high-tech cluster and innovation capacity, and the overall effect of promotion, but there is a marginal decreasing, probably because of the crowding effect or over-competition of the high-tech cluster in some regions; 3) After considering the spatial effect, the impact of the high-tech cluster on the innovation capacity of both local and neighboring regions shows a “U” curve, but the spillover to the neighboring areas is relatively limited. Therefore, to give full play to the advantages of the high-tech cluster, it is necessary to take a long-term view when formulating relevant industrial policies while considering the differences in regional economic development levels and spatial spillover effects.