Climate volatility and market uncertainty pose significant challenges to agricultural stability. We assess whether and how agricultural industrial agglomeration shapes China’s agricultural economic resilience using province-level panel data for 2003–2023 and a transparent, entropy-weighted index spanning resistance, recovery, and adaptability. Four results stand out. First, in a two-way fixed-effects model, agglomeration is associated with higher resilience on average, and this finding remains robust across multiple robustness tests and after addressing endogeneity concerns. Second, regional subgroup analyses reveal pronounced heterogeneity, providing evidence for geographically targeted policy design. Third, mechanism analysis reveals that the agricultural research intensity serves as a partial mediator between agglomeration and resilience. Fourth, the agglomeration-resilience relationship is nonlinear—N-shaped in the aggregate, while panel quantile regressions reveal an inverted-U among low-resilience provinces and an N-shaped pattern at the median and upper end of the distribution. In an extension, global Moran’s I statistics for three alternative resilience indices reveal significant positive spatial autocorrelation, indicating that agricultural economic resilience tends to cluster geographically and that spatial spillovers are likely to be present. In conclusion, agglomeration is a net enhancer of agricultural economic resilience, but its payoffs are agglomeration- and distribution-dependent: gains taper or reverse around the mid-range for low-resilience provinces, while the median and upper segments benefit again as specialization deepens, in a setting where resilience itself is spatially clustered. Reinforcing the research channel and tailoring actions to local resilience levels are therefore pivotal.