Abstract: As the“ballast stone”of national food security, the black soil region of Northeast China is experiencing a continuously shrinking population, characterized by rural labor outmigration, urban population stagnation, and an aging agricultural workforce. In this context, exploring the coupling evolution mechanism between agricultural multifunctionality and resilience has become a critical strategic issue. In this study, 21 leagues and cities in the black soil region were taken as research units, utilizing panel data from 2008 to 2022. An evaluation index system was constructed covering 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. The 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 the two systems was then quantified; finally, four typical cases (Changchun, Daqing, Qitaihe, and Xilingol League) were selected to distill the evolution modes and underlying mechanisms. The results demonstrated that agricultural multifunctionality remained relatively stable amidst fluctuations, with an average value of approximately 0.357, effectively serving as a “stabilizer” for the regional agricultural system. Agricultural resilience exhibited a pronounced stepwise upward trend, increasing from 0.285 in 2008 to 0.315 in 2022, representing a cumulative improvement of 10.5%. Notably, the transformative capacity showed the most significant increase, indicating that the system had transitioned from basic functional maintenance to a dynamic adaptation stage through factor reorganization, technological substitution, and structural optimization. The CCD between multifunctionality and resilience showed an overall fluctuating upward trend, with the regional mean increasing from 0.554 to 0.560, maintaining a barely coordinated level. Spatially, a stable pattern of “high in the central core, low in the peripheral areas” emerged, centered on the Harbin-Changchun urban agglomeration. Harbin 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 population shrinkage types. The comprehensive shrinking areas, impacted by the simultaneous outflow of both urban and rural factors, showed sluggish improvement in coupling levels, with resource-based cities like Qitaihe remaining in long-term near-disorder states. The rural-dominant shrinking areas exhibited pronounced path dependence, where factor substitution efficiency—particularly the replacement of labor by capital and technology—determined the success of systemic transformation. Jiamusi successfully transitioned from barely coordinated to primary coordinated, while Shuangyashan showed limited improvement, highlighting divergent transformation pathways under similar population pressures. Based on the spatiotemporal differentiation patterns and the comparative analysis of typical cases, four typical evolution modes were distilled: growth pole leading, capital-technology substitution, systemic recession, and development decoupling. Furthermore, four underlying mechanisms were revealed: structural empowerment, path dependence, low-level locking, and transmission blockage. These findings can provide a theoretical basis and empirical reference for formulating differentiated agricultural policies under the context of population shrinkage, emphasizing the need for factor reallocation, technological substitution, and institutional innovation tailored to specific regional conditions.