Background: 3D facial scanning has changed the way facial aesthetic is evaluated and has numerous advantages for facial analysis. The specific relationship between lip vermilion morphological changes after orthodontic extraction treatment has not been fully explained. The objective of this study was to evaluate 3D morphological changes after orthodontic extraction treatment in lip vermilion of adult females with dentoalveolar protrusion using a structured light-based scanner. Methods: Forty-two female subjects (25.2 ± 1.9 years) were recruited as the treatment group; these patients had undergone extraction treatment and achieved better sagittal profiles. Twenty female subjects (25.5 ± 2.1 years) were enrolled in the non-treatment group; these patients did not require any orthodontic treatment. The follow up time for the treatment group was more than 24 months and for the non-treatment group was more than 12 months. 3D facial scans were captured using 3D CaMega. Six landmarks (Ls, Li, R.Chp, L.Chp, R.Ch, and L.Ch), three linear measurements (mouth height, philtrum width, and mouth width), and three area measurements (upper, lower, and total vermilion area) were measured. The spatial deviations of the three volumetric measurements (upper, lower, and total vermilion) were constructed for quantitative analysis. Superimposed colour maps and spectra were constructed for visual analysis of morphological changes as a qualitative evaluation. Results: Mouth height and philtrum width decreased (-0.93mm and -1.08mm, respectively) significantly (p=0.008 and p=0.027, respectively), and no significant (p=0.488) change in mouth width was observed in the treatment group. The lower and total vermilion surface areas decreased (-51.00mm2 and -69.82mm2 , respectively) significantly (p=0.003 and p=0.031, respectively) in the treatment group, but the upper vermilion remained unchanged (p=0.752). In the treatment group, significant retractions were observed in the superimposed colour maps and spectra, and the volumetric measurements of the vermilion changed significantly (p=0.012, p=0.001 and p=0.004, respectively). Significant differences were found between the treatment group and the non-treatment group in linear, area and volumetric measurements. Conclusions: This study established a method for qualitative and quantitative evaluation of the lip vermilion. Significant 3D retraction of the lip vermilion after the extraction treatment was found, with morphological variation between upper and lower vermilion.