Reference scenarios serve as a foundational benchmark for evaluating the mitigation potential of technological options and policy proposals, and their specifications play a critical role in ensuring accurate and policy-relevant assessments. Leveraging the Agricultural non-CO2 Greenhouse gAs InveNtory (AGAIN) model, this study assessed the mitigation potential of agricultural non-CO2 greenhouse gas (GHG) emissions under technical potential (TP) scenarios relative to four reference scenarios: China-specific business-as-usual (CBAU), Shared Socioeconomic Pathway 2 (SSP2), and two current policy scenarios (CP-CBAU and CP-SSP2). The results indicated that both socioeconomic assumptions and current policy inclusion substantially influenced emission trajectories and mitigation estimates. Under the CBAU scenario, emissions were projected to rise continuously, reaching 1161 MtCO2eq by 2060. In contrast, emissions under the SSP2, CP-CBAU, and CP-SSP2 scenarios were expected to peak between 2042 and 2050 at levels ranging from 1017 to 1109 MtCO2eq. Excluding current mitigation policies led to an overestimation of mitigation potential by 42–52 %, while differences in socioeconomic assumptions contributed to a smaller uncertainty of approximately 7 %. Although the choice of reference scenario had a limited impact on the regional prioritization of mitigation efforts, it significantly affected the prioritization of mitigation subsectors. Furthermore, the influence of reference scenario selection on mitigation potential assessments varied spatiotemporally, with greater effects observed in the long term and in provinces that had not yet peaked in emissions by 2023. These findings underscore the need to enhance the diversity, timeliness, and transparency of reference scenario design to support robust mitigation strategy development and policy evaluation.