Climate change has become a global issue of general concern to human society. It is not only an environmental issue, but also a development issue. As the second largest economy in the world, China has adhered to its commitments in the Paris Agreement and formulated a series of autonomous action targets. In this context, scholars have done a lot of research focusing on carbon emission reduction, but have neglected the spatial correlation of carbon emission, and lack of research on carbon emission reduction in urban agglomerations. The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) has been at the forefront of China in terms of economy, politics, ecology, and civilization by taking advantage of the “one country, two systems” policy. This article innovatively proposes that there is a non-linear relationship between the efficiency of green innovation and the carbon emission intensity of the Guangdong-Hong Kong-Macao GBA, and has passed quantitative verification. Based on the panel data of the Guangdong-Hong Kong-Macao GBA from 2009 to 2019, we used the super-efficiency slacks-based measure (SBM) model to measure the efficiency of green innovation. We used the global Moran index and Theil index to discuss the spatial correlation of carbon emissions and regional differences in carbon emission intensity in the Guangdong-Hong Kong-Macao GBA, respectively. Then, we used the threshold model to verify the nonlinear relationship between the efficiency of green innovation and the intensity of carbon emissions in the Guangdong-Hong Kong-Macao GBA. The results of the study found that the green innovation efficiency of the Guangdong-Hong Kong-Macao GBA is increasing overall, carbon emissions have a certain spatial correlation, and the correlation is low overall. The impact of green innovation efficiency on carbon emission intensity has a non-linear relationship and there is an “inverted U” pattern between the two, and there is an inflection point in green innovation efficiency. Based on this, this article proposes carbon emission reduction measures within a reasonable range, and looks forward to future research directions and complement the research deficiencies.