Two-dimensional (2D) intraoral ultrasonography has shown promising potential to image the periodontal structures without the ionizing radiation. To advance the clinical application of intraoral ultrasonography, a novel ultrasound imaging system is necessary to image the structure of periodontal anatomy in 3D space. In this study, we developed a portable 3D intraoral imaging system by consisting of a handheld high-frequency linear intraoral ultrasound transducer (up to 23 MHz) and an optical tracking system. The proposed system can consistently provide the 2D images with 3D poses information for the real-time online reconstruction. After the online reconstruction, a total variation regularization (TVR) technique was adopted to filter the noise in raw tracking poses during the freehand scanning. The validation was performed on two incisors of a mandibular phantom, and the reconstructed volume from the proposed system was compared with the volume from Micro Computed Tomography (μCT). The global average absolute and relative errors measured on the width and height of the two incisors were 0.16±0.06 mm and 2.63±1.50%, respectively. The TVR-corrected reconstructed volumes revealed a smoother reconstructed surface. This in-vitro study demonstrated a comparable result of the proposed system with μCT to image the dental phantom.