The invention provides a high precision propellant filling method for a high orbit satellite with parallel-connection flat-laid storage tanks. The high precision propellant filling method comprises the steps that before test, a standard weight is used for calibrating a barycenter test board; the satellite is directly mounted on the barycenter test board, and before a propellant is filled, influence, of tools on the periphery of the satellite, on the test is eliminated; in the filling process, the mass and the barycenter of the satellite are directly measured; and after filling, the creeping effect of the barycenter test board is calibrated, and test is conducted again. By adoption of the filling method provided by the invention, the precision of mass test is smaller than 0.6 kg, the precision of barycenter test is smaller than 0.5 mm, the error of satellite filling is decreased, the determination precision, of the transverse barycenter of the satellite, on the ground is increased, a direct basis is provided for determination of the transverse barycenter position of the satellite at the ignition time of an orbit transfer section apogee engine, control over disturbance torque is facilitated, and safe orbit transfer can be ensured.