Irinotecan (CPT-11) is a camptothecin chemotherapy drug largely used in treating cancers. However, its strong adverse effects, such as gastrointestinal and hepatic toxicities, tend to reduce the patients’ life qualities and to limit the clinical use of CPT-11. The protective roles of selenium (Se) and probiotics against CPT-11-induced toxicity have been widely reported. However, the application of Se-enriched probiotics in the adjuvant therapy of CPT-11 has not been well explored. The purpose of this study is to evaluate the in-vitro and in-vivo effects of Se-enriched Bifidobacterium longum DD98 (Se-B. longum DD98) as a chemotherapy preventive agent on alleviating intestinal and hepatic toxicities induced by CPT-11 chemotherapy. The results showed that Se-B. longum DD98 positively regulated the aberrant cell viability and oxidative stress induced by CPT-11 both in human normal liver (L-02) and rat small intestinal epithelial (IEC-6) cell lines. In vivo experiment revealed that Se-B. longum DD98 significantly attenuated intestinal and hepatic toxicities by ameliorating symptoms such as body weight loss and diarrhea, and by improving the biochemical indicators of hepatotoxicity and oxidative stress. Furthermore, we discovered that the protective effects of Se-B. longum DD98 based largely upon decreasing the pro-inflammatory cytokines IL-1β and IL-18 and enhancing the expression of tight-junction proteins occludin and ZO-1, as well as restoring the composition and diversity of gut microbiota. Results suggested that Se-B. longum DD98 effectively protected livers and intestines against the CPT-11-induced damages, and therefore, could be considered as a promising adjuvant therapeutic agent with CPT-11 for the cancer treatment.