OBJECTIVE To compare the clinical and radiological outcomes of O-arm navigation assisted percutaneous pedicle fixation and open freehand pedicle fixation in treatment of AO type A3 thoracolumbar burst fractures (TBFs) without neurological deficit. METHODS This retrospective study involved 72 patients with type A3 TBFs who underwent O-arm navigation assisted percutaneous pedicle fixation (MIS group) or open freehand posterior pedicle fixation (OPPF group) from September 2015 to December 2017. Demographic data and clinical characteristics were comparable between these two groups before surgery. Operating time, intraoperative blood loss, and the time of hospitalisation stay were analysed. Visual analog scale (VAS) scoring and Oswestry disability index (ODI) was assessed for each patient pre- and postoperatively. Radiographic follow-up was assessed by the Local kyphosis angle (LKA), Vertebral wedge angle (VWA), and Anterior body height (ABH). The accuracy of screw placement was examined by computed tomography. RESULTS The two groups were matched in terms of demographic and clinical features. Intraoperative blood loss was significantly less in the MIS group compared to the OPPF group (p < 0.05). The average time for hospitalisation stay in the MIS group was significantly shorter than OPPF group (p < 0.05). However, the operative time revealed no significant difference between two groups (p > 0.05). Meanwhile, the VAS score and ODI score in the MIS group were significantly lower than that in the OPPF group after surgery (p < 0.05). Radiographic assessments revealed no obvious difference between the 2 groups immediately after surgery or at the final follow-up (p > 0.05); The accuracy rate of pedicle screw position in the MIS group was higher than OPPF group (97.8% vs 78.5%, respectively; p < 0.001). No deep wound infection, additional surgery, implant failure, or neurological complications were recorded in either group. CONCLUSIONS Percutaneous short-segment pedicle instrumentation assisted with O-arm navigation represents an effective and safe alternative for type A3 TBFs. It has several advantages compared with open approach, including less blood loss, shorter hospitalisation, less postoperative pain, higher accuracy of pedicle screw placement, and faster recovery period in treating TBFs. However, it requires a longer learning curve and long-term results have to be studied in other well-designed studies. Percutaneous short-segment pedicle instrumentation assisted with O-arm navigation represents an effective and safe alternative for type A3 TBFs. The utilization of O-arm navigation and percutaneous pedicle screw fixation guaranteed the high accuracy of screw placement, protected staff from radiation exposure and offered benefits of minimal invasive technique.