The invention discloses a calibration method and system for a non-orthogonal error of a gyroscope. The method comprises the steps that step S110, each axial non-orthogonal error of the gyroscope on aninitialized cradle head is zero, and each joint angle of each shaft of the cradle head is controlled at an initial zero position; S120, one shaft of the cradle head is controlled to rotate a preset angle in the corresponding axial direction, and the rotation frequency is updated; step 130, a change value of the joint angle of each shaft of the cradle head and each axial angular velocity measuredby the gyroscope are acquired, an axial non-orthogonal error of a rotating shaft is calculated, and each axial angular velocity is calibrated; S140, whether or not preset conditions are met is judged,if not, S120 is returned to be executed; if yes, the shaft is controlled to return to the initial zero position; S150, whether or not the calibration of each shaft is completed is judged, and if not,other shafts are controlled to be subjected to S120-S140, and if yes, ending is conducted. The calibration method and system for the non-orthogonal error of the gyroscope directly calibrate the non-orthogonal error by arranging the gyroscope on the cradle head to avoid the influence of the installation error.