Abstract: Agriculture is not only a significant source of carbon emissions but also a massive carbon sink system. Reducing carbon emissions and increasing carbon sinks are essential directions and goals for achieving the green and high-quality development of modern agriculture. Protected agriculture is a crucial symbol of modern agriculture in China, revealing its spatiotemporal pattern evolution and the effect of reducing carbon emissions and increasing carbon sink is of great significance for achieving the “double carbon” goal and promoting green transformational development. However, there is limited research on reducing carbon emissions and increasing carbon sinks in protected agriculture, and the spatial correlation among protected agriculture, carbon emissions, and carbon sinks has not received enough attention. Research on reducing carbon emissions and increasing carbon sinks in protected agriculture should be conducted using a more microscopic county-level sample and should consider the heterogeneity of location and grain-production areas. Based on a comprehensive review of the existing literature, this study applies spatial econometric methods and utilizes panel data from 1828 counties in China from 2013 to 2017 for statistical analysis and empirical research. First, this study analyzed the temporal characteristics and spatial correlations of carbon emissions, carbon sinks, and protected agriculture at county level. Subsequently, it empirically analyzed the impact of protected agriculture on carbon emissions and sinks. Based on this, further analyses were conducted from the perspective of regional and grain-production area heterogeneity. The results showed that 1) carbon emissions in Chinese counties exhibited an overall pattern of higher levels in the east and lower levels in the west, while carbon sinks showed the opposite pattern. The spatial pattern of protected agriculture area followed the same trend as carbon emissions, and all three variables exhibited significant positive spatial correlations. A high-high agglomeration of carbon emissions was concentrated in the eastern region, with the center of gravity leaning towards the northwest. A high-high agglomeration of carbon sinks was concentrated in the western, northeastern and southwestern regions, whereas a high-high agglomeration of protected agriculture was concentrated in the Huang-Huai-Hai Region. 2) Protected agriculture area had a “U”-shaped direct and indirect effect on carbon emissions, indicating a significant carbon reduction effect. However, both the direct and indirect effects of protected agriculture area on carbon sinks were significantly negative, suggesting an insignificant sequestration effect. 3) The roles of protected agriculture in carbon reduction and sequestration exhibited significant heterogeneity. In terms of regional heterogeneity, protected agriculture significantly promoted carbon emission reduction in the eastern and northeastern regions, while significantly inhibiting carbon sinks in the central and western regions. Regarding the heterogeneity in grain-production areas, protected agriculture area had a significant carbon reduction effect in the major grain-production and sales areas, but its sequestration effect was not significant in the three grain-production areas. This study suggests that counties should accelerate the promotion of green development in protected agriculture, develop low-carbon agriculture according to local conditions, strengthen cooperation and communication on carbon reduction and sequestration between regions, effectively promote the green and sustainable development of protected agriculture, and achieve the goals of carbon reduction and sequestration.