Abstract: Promoting mass entrepreneurship and innovation is essential to support implementing the innovation-driven development strategy, and innovation and entrepreneurship ability also affect the regional green development level. This paper selected 101 prefecture-level cities in the Yangtze River Economic Belt from 2003 to 2017 as research samples. Moreover, the impact of regional innovation and entrepreneurship ability on total carbon emissions and carbon intensity in the Yangtze River Economic Belt is analyzed by using a spatial econometric model. The heterogeneity of spatial effects is tested by region and degree of marketization, and finally, the robustness test is conducted to ensure the reliability of the results. Research shows that innovation factor agglomeration plays a significant positive role in carbon emission reduction. In contrast, entrepreneurial factor agglomeration increases regional carbon emissions while reducing carbon emission intensity. In addition, innovation factor agglomeration’s spillover effect can reduce adjacent regions’ carbon emissions and carbon intensity. In contrast, entrepreneurial factor agglomeration will increase the carbon emissions and carbon intensity of adjacent regions. Besides, the marketization degree and geographical location play an important role in influencing the relationship between innovation and entrepreneurship and carbon emissions. According to the empirical conclusions, this paper puts forward corresponding policy recommendations for different regions.