Objective To establish the three-dimensional model of human permanent premolars based on Microcomputed tomography(Micro-CT) data, and evaluate the efficiency quantitatively of two different instrumentations for root canal retreatment. Methods Forty extracted permanent premolars for the reason of orthodontic treatment were collected, prepared by using ProTaper Ni-Ti files and filled by cold gutta pertscha lateral condensation technique. The subjects were scanned by Micro-CT. Forty teeth were randomly divided into two groups and retreated by K-Flexo files and ProTaper Universal retreatment system respectively. Then all subjects were scanned again, and the mean percentage of remaining filling materials and the scores of remaining filling materials presented in upper, middle and apical 1/3 of the canal were calculated. Results Mean percentage of the remaining filling materials by K-Flexo files was lower than that by ProTaper Universal retreatment system(P=0.005). The scores demonstrated that K-Flexo files had greater efficiency than ProTaper Universal retreatment system when retreating the apical 1/3 of canal(P