Objective To compare the measurement differences between the skull 3D printed model and the real specimen under different CT scan slice thicknesses, and to explore the effect of slice thickness on the accuracy of the 3D printed model.    Methods Eight normal skull specimens (marked as Nos. 1-8) (group N) were used for CT scanning with different slice thicknesses, specifically 0.625 mm (group A), 1.25 mm (group B), and 2.5 mm (group C), 3.75 mm (group D), and 5 mm (group E), and then carried out 3D reconstruction and 3D printing respectively, and compared the anatomical reduction degree of the foramen magnum diameter, anterior clinoid distance, and butterfly wing distance of the 3D printed skull model.    Results The reduction degree of anatomical structure of 3D printed skull model decreased with the increase of CT slice thickness. There was no significant difference in the accuracy of 3D model among groups A, B and C ( P>0.05). There was a high correlation between group A, B and C and group N ( P<0.05). The size indexes and statistical values of group A, B and C were similar.   Conclusion CT slice thickness has a significant effect on the accuracy and reduction of the 3D printed skull model. The 3D printed model with thin slice data (0.625mm, 1.25mm, 2.5mm) has higher accuracy and less difference.