To improve the accuracy of a 3D bone position estimation system that displays 3D images in response to changes in the position of fluoroscopic images, modified markers using quick response (QR) codes were developed. The aims of this study were to assess the accuracy of the estimated bone position on 3D images with reference to QR code markers on fluoroscopic images and to compare its accuracy with metal bead markers. Bone positions were estimated from reference points on a fluoroscopic image compared with those on a 3D image. The positional relationships of QR code and metal bead markers on the fluoroscopic image were compared with those on the 3D image in order to establish whether a 3D image may be drawn by tracking positional changes in radius models. Differences were investigated by comparing the distance between markers on the fluoroscopic image and that on the 3D image, which was projected on the monitor. The error ratio, which was defined as the difference in the measurement between the fluoroscopic and 3D images divided by the fluoroscopic measurement, was compared between QR code and metal bead markers. Error ratios for the QR code markers were 5.0 ± 2.0%, 6.4 ± 7.6%, and 1.0 ± 0.8% in the anterior-posterior view, ulnar side lateral view, and posterior-anterior view, respectively. Error ratios for the metal bead markers were 1.3 ± 1.7%, 13.8 ± 14.5%, and 4.7 ± 5.7% in the anterior-posterior view, ulnar side lateral view, and posterior-anterior view, respectively. The error ratio for the metal bead markers was smaller in the initial position (p < 0.01). However, the error ratios for the QR code markers were smaller in the lateral position and the posterior-anterior position (p < 0.05). In QR code marker tracking, tracking was successful even with discontinuous images. The accuracy of a 3D bone position estimation was increased by using the QR code marker system. QR code marker tracking facilitates real-time comparisons of dynamic changes in preoperative 3D and intraoperative fluoroscopic images.