The purpose of this paper is to design a tri-axial attitude balancing control system for the quad-rotor, including roll, pitch and yaw axes. The tri-axial angular velocities were measured by the tri-axial gyroscopes. The roll and pitch angles were measured by the accelerometers. The yaw angle was measured by the magnetometer. The extended Kalman filter (EKF) was used to estimate tri-axial angles and angular velocities, and to filter the vibration noise caused by the actuating motor. Then, three fuzzy controllers were designed to stabilize the tri-axial attitudes respectively. The inputs of the controllers are the filtered tri-axial angles and angular velocities. The outputs of controllers are the pulse width modulation (PWM) signals. This study improves the accuracy of estimation and filtered the vibration noise by adjusting the covariance of extended Kalman filter. Finally, three experiments of the tri-axial attitude control was performed on the quad-rotor vehicle in the indoor environment. The experiment verifies the stabilization effectiveness of the proposed control design respectively.