The Yellow River Basin (YRB), a vital region for agricultural production in China, is currently grappling with severe rural population shrinkage and variations in the carbon emission intensity across the basin. Based on census data from 2010 to 2020, this study categorized 320 counties by population shrinkage type and applied baseline regression and upper–middle–lower reach heterogeneity analysis to explore population shrinkage’s impact on carbon intensity. The results indicated that population shrinkage in the Yellow River Basin during 2010–2020 was primarily characterized by a rural population decline, which exerted divergent impacts on carbon emissions across the basin. Consequently, the upper reaches were identified as a critical problem area where severe population shrinkage coexisted with a high carbon emission intensity. Based on these findings, targeted and region-specific strategies and policies are proposed. Specifically, High Shrinkage-High Emission (H-H) regions need to focus on promoting ecological migration and the coordinated transformation of industries; High Shrinkage-Low Emission (H-L) regions should strengthen policy coordination in the border areas of the middle and upper reaches; Low Shrinkage-High Emission (L-H) regions should promote the low-carbon technological transformation of traditional industries in downstream counties; and Low Shrinkage-Low Emission (L-L) regions should refine the low-carbon transformation model in the core downstream areas.