The diagnosis and treatment of root fractures are difficult issues in dentistry. A three-dimensional swept source optical coherence tomography (OCT) system was constructed. Utilizing cardiovascular endoscopic imaging catheter, we imaged 46 root section samples with root fractures(width ranges from 8 μm to 283 μm). The results show that the system has a diagnostic accuracy as good as 98.3% when the width of root fractures is greater than 30 μm. The diagnostic accuracy is 36.3% for fractures smaller than 30 μm. For the 25 fracture-free samples, the accuracy is 92%. Further analysis suggests optimization of the relative position and angle between the catheter and sample sections, as well as 3D reconstruction of images. These improvements achieve 100% accuracy for above-30 μm fractures and 57.6% accuracy for below-30 μm ones. This experiment suggests a promising future for the application of endoscopic OCT in the diagnosis of dental root fractures.