Considerable progress has been achieved in the bioaccumulation and transformation of selenium (Se)-enriched lactic acid bacteria (LAB). However, research on the effects of Se on the structure and probiotic potential of LAB is relatively limited. In this study, six industrial LAB strains, including Lactobacillus plantarum 21,805, Lactobacillus paracasei 20,241, Lactobacillus fermentum 21,828, Lactobacillus casei 23,185, Lactobacillus acidophilus 6064, and Lactobacillus plantarum 6076, were cultured in De Man, Rogosa, and Sharpe (MRS) medium containing Se for three generations. High-Se LAB was screened based on bacterial biomass, viable bacterial count, and Se content. Their structural characteristics were analyzed using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). The results indicated that LAB growth was influenced by the Se environment, with high Se (20 μg/mL) inhibiting it. At a Se concentration of 10 μg/mL, LAB maintained integrity and exhibited a high Se enrichment ability, with a Se enrichment of 4.88 ± 0.39 mg/g. The intracellular Se existed in an amorphous or non-crystalline form. Furthermore, Se-enriched LAB exhibited enhanced probiotic properties, including tolerance to simulated gastrointestinal fluids, acid resistance, bile salt resistance, and hydrophobicity. Therefore, Se-enriched LAB are expected to develop new functional foods or dietary supplements for human and animal consumption.