PurposeThe COVID-19 pandemic has profoundly impacted small and medium-sized enterprises (SMEs), inherently vulnerable entities, prompting a pivotal question of how to enhance SMEs’ organizational resilience (OR) to withstand discontinuous crises. Although digital innovation (DI) is widely acknowledged as a critical antecedent to OR, limited studies have analyzed the configurational effects of DI on OR, particularly stage-based analysis.Design/methodology/approachUnderpinned by the dynamic capabilities view, this study introduces a multi-stage dynamic capabilities framework for OR. Employing Latent Dirichlet Allocation (LDA), digital product innovation (DPI), digital services innovation (DSI) and digital process innovation (DCI) are further deconstructed into six dimensions. Furthermore, we utilized fuzzy-set qualitative comparative analysis (fsQCA) to explore the configuration effects of six DI on OR at different stages, using data from 94 Chinese SMEs.FindingsFirst, OR improvement hinges not on a singular DI but on the interactions among various DIs. Second, multiple equivalent configurations emerge at different stages. Before the crisis, absorptive capability primarily advanced through iterative DPI and predictive DSI. During the crisis, response capability is principally augmented by the iterative DPI, distributed DCI, and integrated DCI. After the crisis, recovery capability is predominantly fortified by the iterative DPI, expanded DPI and experiential DSI. Third, iterative DPI consistently assumes a supportive role in fortifying OR.Originality/valueThis study contributes to the extant literature on DI and OR, offering practical guidance for SMEs to systematically enhance OR by configuring DI across distinct stages.