The realization pathway of agricultural ecological product value serves as a crucial and indispensable link for achieving balanced, coordinated, and sustainable development between the agricultural economy and the broader resource–environment system. A well-designed and properly structured combination of these pathways can help effectively balance economic growth, ecological protection, and resource utilization efficiency in agricultural activities. Through this process, it can stimulate the green upgrading and gradual transformation of agricultural production, thereby promoting a long-term improvement in agricultural green total factor productivity (AGTFP). However, existing studies remain limited in scope, and only a few have systematically examined or empirically tested the specific impacts of individual realization pathways and their combined configurations on AGTFP. This study utilized panel data from 31 provinces in China spanning the period from 2018 to 2022. A super-efficiency SBM model was employed to measure AGTFP, systematically analyze its spatiotemporal evolution and regional disparities, and further explore the configuration pathways contributing to AGTFP improvement using dynamic qualitative comparative analysis (QCA). The main findings of this paper were listed as follows: (1) The empirical results reveal that AGTFP in China has generally demonstrated a clear and steady upward trend over time, with an average annual value of 0.933. In spatial terms, it displays a distinct and relatively stable distribution pattern, characterized by higher levels concentrated in the southwestern regions and relatively lower levels prevailing in the northern parts of the country. (2) High AGTFP resulted from the combination of multiple conditional variables, with market-government collaborative pathways for realizing agricultural ecological product value proving to be the most effective. (3) Four configuration pathways were identified as leading to high AGTFP, which were grouped into two categories: those centered on green financial support and those integrating green finance with compensation for ecosystem services. Notably, green finance emerged as the key driver across all effective configurations. (4) Compared with food crops, the realization of cash crop value contributed more effectively to boosting AGTFP; similarly, green financial support was more effective than rural tourism, and compensation for regulatory services yielded greater improvements than that for support services. (5) From a policy perspective, it is therefore essential to strengthen top-level central coordination and overall policy coherence, improve and expand green finance support mechanisms, and optimize the design and integration of ecological product value realization pathways in a region-specific and context-sensitive manner. These measures will collectively contribute to the comprehensive enhancement and sustained growth of AGTFP across China.