Innovation is an important means to maintain the competitiveness of enterprises and improve the enterprise value. Industrial characteristic affects the R&D activities. Taking 44 electronic and 39 biomedical enterprises of the GEM as a sample, this paper analyze the relationship between the industry nature, innovation performance and enterprise value. The results show that technological innovations have important impact on the market value of enterprises, and the different industries have various industry characteristics. Electronic enterprises have more innovation outputs than biomedical enterprises. A U-shaped relationship was found between patents number and firm value in biomedical industry, but the inverse U Curve listed in electronic industry. The distribution of core technology area in electronic industry is more scattered, and the impact of patents creativity on electronic enterprises’ value is almost negligible. Instead, it requires higher creativity of patents in biomedical industry, and the innovativeness of patents has greater influence on the enterprises’ performance. Incremental innovation is the main innovation pattern in electronic industry, and biomedical enterprises have shifted emphasis to make breakthrough in fundamental innovation. The enterprise should take into full account of industrial heterogeneity in technology innovation, and allocate resources efficiently to improve the innovation performance.