It was the focus of attention that probiotic control drink was packed with prebiotic nutrients and lactic acid bacteria. So, this study is aimed at revealing that the fermented carrot pulp regulation and protection function to the intestinal microecological disorders usually induced by antibiotic treatment. First, we study on lactobacillus fermentation conditions and effects on the secondary metabolism of fermented carrot juice, get its phenolic acids up, and get its flavonoids down. Then, establishment of the dysbacteriosis mouse model was used to validate the fermented carrot pulp prevention and treatment of intestinal microbiota imbalance. After the antibiotic treatment, the mice showed impotence, laziness, slow movement, weight loss, thin feces, dull hair, and anal redness, while the mice in the control group were all normal in terms of the mental state, diet, weight, and bowl movement. Along with the treatment, the abnormal conditions of the mice in the model group and natural recovery group improved in different degrees, indicating that the fermentation treatment is of help to the intestinal microbiota recovery. The fermentation-treated group of mice recovered close to normal that the diarrhea disappeared, and the weight gain, mental state, and the feces became normal. The serum antioxidant (SOD, GSH, and MDA) levels of the mice were checked. The superoxide dismutase (SOD) levels and glutathione (GSH) levels in the ordinary fermentation-treated group and probiotic fermentation-treated group were significantly increased compare to the natural recovery group. The malondialdehyde (MDA) levels showed great differences between the fermentation-treated groups and the blank group. At last, the 16sRNA analysis revealed that the microbiota richness and diversity in probiotic fermentation (J) are much higher than those in the model group (H), ordinary fermentation group (I), and blank group (G). Groups J and I are of significantly higher antioxidant level than group H; however, only the glutathione (GSH) level in group J increased dramatically but not those in the other three groups. Antibiotic treatment-induced mouse intestinal microecological disorder reduce the microbiota richness and diversity. Prebiotics fermented carrot pulp treatment can help in the recovery from the microbiota richness and diversity level prior to the antibiotic treatment, which suggests it can regulate and protect the murine intestinal microbiome.