Previous studies found relationship between fluoride exposure and lipid metabolism. In present study, a cross-sectional study was conducted. Urinary fluoride concentrations and lipid metabolism indicators were tested. Single nucleotide polymorphisms of ATP2B1 were sequenced. The median of urinary fluoride was 1.32 mg/L. Urinary fluoride was positively associated with the decrease in serum ApoA1 (OR = 1.48 [95% CI, 1.27-1.72]), inversely with ApoB elevation (OR = 0.69 [95% CI, 0.59-0.80]). Rs12817819 with carriers of T allele was associated with the decrease in serum ApoA1 (OR = 0.46 [95% CI, 0.26-0.81]), but inversely in rs17249754 with carriers for A allele (OR = 1.48 [95% CI, 1.07-2.06]) and rs7136259 with carriers for T allele (OR = 1.70 [95% CI, 1.22-2.37]). There was an interaction between urinary fluoride which was lower than 0.9 mg/L and rs7136259 for carriers of T allele (OR = 2.67 [95% CI, 1.34-5.31]) in serum ApoA1 decrease. It indicated fluoride exposure might be associated with the alteration of serum ApoA1 and ApoB in adults.