The Black soil region of Northeast China is the “ballast stone” of national food security. However, a continuously shrinking population is characterized by rural labor outmigration, urban population stagnation, and an aging agricultural workforce. It is often required to explore the coupling evolution between agricultural multifunctionality and resilience. This study aims to clarify agricultural "function-resilience" coupling evolution and its mechanism in the black soil region of northeast China under population shrinkage. 21 leagues and cities were taken as research units. Panel data were then collected from 2008 to 2022. An evaluation index system was constructed to cover four dimensions of agricultural multifunctionality (product supply, economic development, social security, and ecological services) and three dimensions of agricultural resilience (resistance, adaptability, and transformability), totaling 40 indicators. Coupling coordination degree (CCD) model, kernel density estimation, and typical case induction were employed for empirical analysis. A three-step analytical strategy was implemented to evaluate the performance. A parallel comparative analysis was conducted on the spatiotemporal evolution of multifunctionality and resilience; The CCD between two systems was then quantified; Finally, four typical cases (Changchun, Daqing, Qitaihe, and Xilingol League) were selected to distill the evolution modes and mechanisms. The results demonstrated that agricultural multifunctionality remained stable amidst fluctuations, with an average of 0.357, effectively serving as a “stabilizer” for the regional agriculture. Agricultural resilience exhibited a pronounced stepwise upward trend g from 0.285 in 2008 to 0.315 in 2022, thus representing a cumulative improvement of 10.5%. Notably, the transformative capacity showed that there was the most significant increase from basic functional maintenance to the dynamic adaptation stage after factor reorganization, technological substitution, and structural optimization. The CCD between multifunctionality and resilience showed that the regional mean increased from 0.554 to 0.560, indicating an overall fluctuating upward trend with a barely coordinated level. Spatially, there was a stable pattern of “high in the central core, low in the peripheral areas”, which centered on the Harbin-Changchun urban agglomeration. Harbin City achieved a moderately coordinated level (0.719), followed by Daqing (0.672), Suihua (0.655), Changchun (0.642), and Jiamusi (0.610) at the primary coordinated level. In contrast, marginal areas, such as Xilingol League (0.453) and Qitaihe (0.414), remained trapped in an “on the verge of disorder” state. Significant differentiation was observed among areas with different types of population shrinkage. The shrinking areas were impacted by the simultaneous outflow of both urban and rural factors, indicating sluggish improvement in coupling levels, particularly with resource-based cities, like Qitaihe, in long-term near-disorder states. The rural-dominant shrinking areas exhibited pronounced path dependence, where factor substitution efficiency-particularly the labor replacement by capital and technology was used to determine the systemic transformation. Jiamusi City successfully transitioned from barely to primarily coordinated, while Shuangyashan City showed limited improvement, highlighting divergent transformation pathways under similar population pressures. According to the spatiotemporal differentiation patterns and the comparative analysis of typical cases, four evolution modes were distilled: growth pole leading, capital-technology substitution, systemic recession, and development decoupling. Furthermore, four mechanisms were revealed: structural empowerment, path dependence, low-level locking, and transmission blockage. These findings can provide a theoretical basis and empirical reference to formulate differentiated decision-making under the context of population shrinkage, particularly for factor reallocation, technological substitution, and institutional innovation under regional conditions.