Many "hot spot" geographic areas around the world with soils and crops co-polluted with cadmium (Cd) and fluorine (F), two of the most representative pollutants in the environment. However, it still exists argumentative on the dose-effect relationship between F and Cd so far. To explore this, a rat model was established to evaluate the effects of F on Cd-mediated bioaccumulation, hepatorenal dysfunction and oxidative stress, and the disorder of intestinal microbiota as well. 30 healthy rats were randomly assigned to Control group (C group), Cd 1 mg/kg (Cd group), Cd 1 mg/kg and F 15 mg/kg (L group), Cd 1 mg/kg and F 45 mg/kg (M group), and Cd 1 mg/kg and F 75 mg/kg (H group) for 12 weeks by gavage. Our results showed that Cd exposure could accumulate in organs, cause hepatorenal function damage and oxidative stress, and disorder of gut microflora. However, different dosages of F showed various effects on Cd-induced damages in liver, kidney, and intestine, and only the low supplement of F showed a consistent trend. After low supplement of F, Cd levels were declined by 31.29% for liver, 18.31% for kidney, and 2.89% for colon, respectively. The serum aspartate aminotransferase (AST), blood urea nitrogen (BUN), creatinine (Cr), and N-acetyl-beta-glucosaminidase (NAG) were significantly reduced (p < 0.01); The activity of superoxide dismutase (SOD) was elevated and mRNA expression level of NAD(P)H quinone oxidoreductase 1 (NQO1) was decreased in the liver and kidney (p < 0.05). Moreover, low F dosage up-regulated the abundance of Lactobacillus from 15.56% to 28.73% and the 6.23% of F/B ratio was declined to 3.70%. Collectively, this highlights that low dosage of F might be a potential strategy to ameliorate the hazardous effects by Cd-exposed in the environment.