To possess sufficient compliance while keeping an acceptable stiffness level for manipulation with precision, transoral robotic surgery (TORS) demands a flexible robotic system with variable stiffness as presented in this paper. In our study, a flexible 3-PU parallel mechanism employs super-elastic Nickel-Titanium (Ni-Ti) rods to achieve compliant movements beyond the conventional rigid-body parallel mechanisms. With a compact structure and flexible-shaft transmission, the adjustable tube-based variable-stiffness (VS) mechanism allows the stiffness of the manipulator to be continuously tuned in real time according to the surgical requirements. A stiffness model is derived to evaluate the stiffness of the manipulator quantitatively. A parallel mechanism with three prismatic-revolute-spherical (3-PRS) chains is adopted as the master device, to improve the maneuverability and decrease the learning curve for less experienced surgeons. The TORS manipulators are characterized and verified in the laboratory and cadaveric trials, showing the variable stiffness and the execution of the master-slave teleoperated configuration. Furthermore, the cadaveric trials attested the effectiveness of the VS mechanism and the preclinical feasibility of the robotic system.