[Background] Clostridium perfringens ε toxin (ETX) is an enterotoxin produced by C. perfringens type B and D, which is rapidly fatal and economically destructive. [Objective] Our study aimed to investigate the damage of ETX on multiple organs in mice and the difference of binding capability in different intestinal segments. [Methods] The mScarlet-ETX coupled with red fluorescence was constructed and visualized with in vivo imaging system to observe its accumulation in vivo. The combination of ε toxin on various organs and different intestinal segments of mice and the damage to organs were analyzed by pathological sectioning. [Results] It was found that after infection with C. perfringens, the produced ETX could accumulate in the brain, kidney, lung, liver, spleen, heart tissues and caused damage to these organs. ETX in the small intestine of mice was mainly accumulated in the colon. [Conclusion] These results indicated that C. perfringens ε toxin could cause damage to multiple organs and mainly absorbed in the colon, which provided a theoretical basis for the treatment and prevention of C. perfringens containing the epsilon toxin gene infection.