Backgrounds: Intraoral scanner (IOS) accuracy is commonly evaluated using full-arch surface comparison, which fails to take into consideration the starting position of the scanning (scan origin). Previously a novel method was developed, which takes into account the scan origin and calculates the deviation of predefined identical points between references and test models. This method may reveal the error caused by stitching individual images during intraoral scan. This study aimed to validate the novel method by comparing the trueness of seven IOSs (Element 1, Element 2, Emerald, Omnicam, Planscan, Trios 3, CS 3600) to a physical impression digitized by laboratory scanner which lacks linear stitching problems. Methods: Digital test models of a dentate human cadaver maxilla were made by IOSs and by laboratory scanner after polyvinylsiloxane impression. All scans started on the occlusal surface of the tooth #15 (universal notation, scan origin) and finished at tooth #2. The reference model and test models were superimposed at the scan origin in GOM Inspect software. Deviations were measured between identical points on three different axes, and the complex 3D deviation was calculated. The effect of scanners, tooth, and axis was statistically analyzed by the generalized linear mixed model. Results: The deviation gradually increased as the distance from scan origin increased for the IOSs but not for the physical impression. The highest deviation occurred mostly at the apico-coronal axis for the IOSs. The mean deviation of the physical impression (53 ± 2 μm) was not significantly different from the Trios 3 (156 ± 8 μm) and CS 3600 (365 ± 29 μm), but it was significantly lower than the values of Element 1 (531 ± 26 μm), Element 2 (246 ± 11 μm), Emerald (317 ± 13 μm), Omnicam (174 ± 11 μm), Planscan (903 ± 49 μm). Conclusions: The physical impression was superior compared to the IOSs on dentate full-arch of human cadaver. The novel method could reveal the stitching error of IOSs, which may partly be caused by the difficulties in depth measurement.