Against the backdrop of increasing consumer demand for high-quality agricultural products at the consumer end and external shocks faced by agricultural markets, evaluating the influence of organic certification on the market resilience of smallholder farmers holds significant practical significance. Drawing on the concept of “resilient smallholder farmers”, we construct indicators representing market resilience based on two periods of apple sales price data. We systematically analyze the mechanisms through which organic certification affects market resilience and conduct an empirical test, using a sample of 681 apple farmers from the dominant apple-producing region in the Loess Plateau and a multidimensional fixed-effects linear regression model. The research finds that organic certification contributes to the enhancement of market resilience for smallholder farmers, and this conclusion still holds after robustness checks and addressing potential endogeneity concerns. Based on cost-benefit theory, mechanism analysis reveals that organic certification enhances farmers’ cost control capabilities and stability in agricultural returns: the former is manifested by an increase in the probability of using organic fertilizers and biopesticides, while per-acre expenditures on fertilizers and pesticides remains unchanged; the latter is demonstrated by the improvement of apple quality due to organic certification, leading to increased premium capacity and expanded sales channels. Heterogeneity analysis reveals that the market resilience improvement is more pronounced for farmers with better economic conditions, those who join cooperatives, and those located in areas where regional public brands for agricultural products are being developed. Therefore, it is suggested to continue advancing the development of organic agriculture to enhance farmers’ resilience against external shocks and market risks, and to provide feasible solutions for "smallholder farmers” to better access the “big market”.