The information in the literature on the effect of printing layer thickness on interim 3D-printed crowns is limited. In the present study, the effect of layer thickness on the trueness and margin quality of 3D-printed composite resin crowns was investigated and compared with milled crowns. The crowns were printed in 3 different layer thicknesses (20, 50, and 100 μm) by using a hybrid resin based on acrylic esters with inorganic microfillers or milled from polymethylmethacrylate (PMMA) discs and digitized with an intraoral scanner (test scans). The compare tool of the 3D analysis software was used to superimpose the test scans and the computer-aided design file by using the manual alignment tool and to virtually separate the surfaces. Deviations at different surfaces on crowns were calculated by using root mean square (RMS). Margin quality of crowns was examined under a stereomicroscope and graded. The data were evaluated with one-way ANOVA and Tukey HSD tests. The layer thickness affected the trueness and margin quality of 3D-printed interim crowns. Milled crowns had higher trueness on intaglio and intaglio occlusal surfaces than 100 μm-layer thickness crowns. Milled crowns had the highest margin quality, while 20 μm and 100 μm layer thickness printed crowns had the lowest. The quality varied depending on the location of the margin.