Endemic fluorosis is a systemic chronic disease caused by excessive intake of fluoride. It is widely accepted that oxidative stress is closely related to fluorosis; however, molecular mechanism of oxidative stress in fluorosis remains unclear. This study investigated the effects of fluoride (F) on oxidative stress markers of lipid, gene, and protein in rats for revealing molecular mechanism of oxidative stress in fluorosis. The results showed concentration and exposure time of fluoride both had a significant effect on MDA and 8-OHdG. Fluoride concentration significantly impacted AGEs level, but exposure time did not. AOPP was not statistically different among the groups. AGEs decreased with the increase of fluoride in the rats with 3 months of fluoride treatment. The correlation analysis showed the degree of dental fluorosis was significantly negatively correlated with 8-OHdG at 1 month and 3 months, and negatively correlated with AGEs at 3 months. In the rats with 100 mg/L of fluoride treatment, MDA was significant positively correlated with 8-OHdG, and negatively correlated with AGEs. 8-OHdG was significantly negatively correlated with AGEs in the control group and 100 mg/L fluoride group. Taken together, fluoride had different effects on oxidative stress markers of lipid, gene, and protein. Excessive fluoride could increase MDA content, and decrease 8-OHdG and AGEs. These findings suggest that oxidative stress involved in molecular pathogenesis of fluorosis is complicated, and needs to furtherly study in the future.