The invention discloses a sixteen-position error modulation method of a dual-axis rotation inertial navigation system. The method comprises the following steps: determining a carrier coordinate system, determining a rotating axis, determining a rotating coordinate system, defining constant errors, calibration factor errors and installation errors of a gyroscope and an accelerometer, determining arotational angular velocity, a position stopping frequency and a rotational angular velocity, sequentially determining rotating axes, rotating directions, rotating angles and stopping times under 1-16rotating orders, determining an attitude error within one rotating period, determining a velocity error within one rotating period, and determining long-endurance latitude and longitude errors. Underthe condition that the system cost and complexity are not increased, by changing the rotating orders of sixteen positions, an attitude error and a velocity accumulation error within one rotating period of the system are effectively reduced, and simultaneously, the oscillation amplitudes of the caused latitude and longitude errors are obviously reduced, thereby further improving the navigation accuracy of the dual-axis rotation inertial navigation system.