Objective To study the clinical effect of manipulation in the treatment of cervical vertigo due to atlantoaxial joint disorder. Methods A total of 86 patients in our hospital from year of July, 2010 to 2014, with cervical vertigo due to atlantoaxial joint disorder were divided into a control group and a treatment group randomly, with 43 patients in each group. The control group was treated by intravenous dripping of betahistine hydrochloride sodium chloride injection, while the treatment group was additionally treated by manipulation on the basis of the control group. The efficacy and symptoms changes together with average blood flow rate of LVA, RVA, BA, and the value of ADI, VBLADI, and DO were compared between the two groups after one week of the treatment. Results After the treatment, the improvement of vertigo and symptoms of the treatment group was between than the control group(t=12.655, P<0.05); the value of ADI and VBLADI decreased lower in the treatment group than the control group (t were 2.888 and 5.334 respectively, P<0.05);Vm of RVA, LVA and BA increased higher in the treatment group than the control group (t were 4.710, 3.534 and 5.335 respectively, P<0.01). Conclusions Manipulation combined with intravenous dripping of betahistine hydrochloride sodium chloride injection is effective in improving vertigo, decreasing ADI and VBLADI, and correcting atlantoaxial joint disorder.