Senecavirus A (SVA) causes clinical blistering and ulcerative lesions resembling foot-and-mouth disease (FMD), often with mixed infections that exacerbate the disease and impact pig industry development. SVA has been demonstrated to induce diarrhea, dehydration and mortality in piglets. However, the underlying mechanisms of SVA-related intestinal infections remain underexplored. In this study, a three-dimensional cultured apical-out porcine intestinal organoid model was constructed, comprising a variety of cell types, including intestinal stem cells, enterocytes, goblet cells, proliferative cells, Paneth cells and enteroendocrine cells. The model demonstrated SVA susceptibility in intestinal epithelial cells through cytopathic effects, viral detection, and replication. The results revealed an infection sequence from enterocytes to enteroendocrine cells, Paneth cells and intestinal stem cells and ultimately to proliferating cells, which identified enterocytes as the primary SVA targets. The presence of stress granules was observed at 4 hours post-infection (hpi), with a notable decline over time, reaching near-disappearance at 20 hpi. At this stage, an innate immune response was evident, with significant upregulation of the interferon IFN-α, the interferon-stimulated gene ISG-15, OAS1, OAS2, the signal transducer and activator of transcription 1 (STAT1), the mucosal immunity gene Muc2, and the cytokine IL-6, which appeared to limit further SVA infection. This study elucidates the infection pattern of SVA in intestinal epithelial cells and reveals the mechanism of interaction. It offers insights for controlling secondary infections.