The spleen is a primary target of deoxynivalenol (DON) toxicity, but its underlying molecular mechanisms remain unclear. This study investigates the effects of DON on inflammation, splenic macrophage polarization, endoplasmic reticulum (ER) stress, and transcriptome changes (mRNA and lncRNAs) in mouse spleen. We found that DON exposure at doses of 2.5 or 5 mg/kg BW significantly induced inflammation and polarized splenic macrophages towards the M1 phenotype. Additionally, DON activated PERK-eIF2α-ATF4-mediated ER stress and upregulated apoptosis-related proteins (caspase-12, caspase-3). The ER stress inhibitor, 4-Phenylbutyric acid, significantly alleviated DON-induced ER stress, apoptosis, and the M1 polarization of splenic macrophages. Transcriptome analysis identified 1968 differentially expressed (DE) lncRNAs and 2664 DE mRNAs in mouse spleen following DON exposure. Functional enrichment analysis indicated that the upregulated genes were involved in pathways associated with immunity, including Th17 cell differentiation, TNF signaling, and IL-17 signaling, while downregulated mRNAs were linked to cell survival and growth pathways. Furthermore, 370 DE lncRNAs were predicted to target 255 DE target genes associated with immune processes, including the innate immune response, interferon-beta response, cytokine production regulation, leukocyte apoptosis, and NF-κB signaling genes. This study provides new insights into the mechanisms underlying DON toxicity and its effects on the immune system.