The construction of ecological barriers in the Yellow River Basin represents a significant step toward reducing agricultural carbon emissions, achieving carbon neutrality, and reaching carbon peaking in China. The diverse agrarian development objectives of various regions within the basin have resulted in a heterogeneous approach to greening agriculture. Therefore, this paper will evaluate the development of carbon sink agriculture across 34 cities and municipalities in the lower Yellow River basin from 2008 to 2021 based on the EBM-GML model, and analyze the spatial-temporal evolution of agricultural green total factor productivity (AGTFP) in each region through the application of the Moran index, kernel density estimation, and spatial Markov chain analysis. The results demonstrate that agricultural carbon emissions in the Lower Yellow River Basin gradually decreased throughout the study period. Furthermore, overall carbon emission efficiency improved, indicating significant potential for further emission reduction. In addition, Agricultural Green Technology Progress (AGTC) has become a primary driver of AGTFP growth, while Agricultural Green Technology Efficiency (AGEC) has demonstrated a gradual upward trend. Locally, most areas are weakly connected and display an isolated development trend. The results of the kernel density analysis demonstrate a notable degree of mobility in the distributional dynamics of AGTFP growth, characterized by a gradual narrowing of the gap between locations. The transfer of (AGTFP) types in the lower reaches of the Yellow River Basin is stable, with a noticeable “club convergence” phenomenon, while geographical conditions significantly influence the transfer of AGTFP types in this region. Based on long-term trend predictions, the future trajectory of AGTFP in the lower Yellow River Basin appears optimistic and is expected to improve progressively, with the overall distribution tending toward equilibrium.