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China’s GEM (Growth Enterprise Market, also named as ChiNext stock market) enterprises are mainly small and medium-sized enterprises in the start-up stage, which have high-speed growth. This work uses three-stage least squares (3SLS) based on combines system equation to study the impact of technological innovation investment, executive incentive, and enterprise financial performance. The results show that in China’s GEM enterprises, R&D in the current period positively affects financial performance in 1% significance level. R&D of the lag period has a significant negative impact on the financial performance of the current period. Conversely, the financial performance of the current period has a significant negative impact on R&D. While both salary incentive and equity incentive will improve financial performance, executives seem to value short-term interests MORE. Executive equity incentive has a significant negative moderating effect ownership due to ownership structure in GEM is needed to strengthen the control right. This work proposes a new research horizon in GEM in China, and can help the GEM design an effective management mechanism to improve the financial performance of the enterprise.