Objective To adopt Cone-beam CT to conduct the comparison among10 midsagittal reference planes which are made by the 5 points S, N, Ba, Cg, PNS, mostly used in the clinical orthodontics, to valuate their accuracy and provide references for the establishment of the CBCT three-dimensional cephalometry facial symmetry analysis system in the future. Methods 53 cases of 12～20-year-old patients with facial symmetry were selected, skull CBCT images were taken, and the facial asymmetry index of each patient was calculated on the basis of 10 kinds of commonly used midsagittal reference planes. Results There was a significant difference among the 10 planes(P﹤0.05), and the facial asymmetry index was the smallest of the midsagittal plane determined by S, N and Ba（11.07±4.146）.Conclusion Based on the results of the CBCT three-dimensional cephalometry, the accuracy of the midsagittal reference plane determined by the S, N, Ba is the highest one.