The present invention provides a fuel filling system and a fuel filling method thereof that can determine the validity of information transmitted from a vehicle side while filling fuel with high accuracy. A hydrogen gas filling method of a hydrogen filling system includes: a step of filling hydrogen gas from a hydrogen station to a hydrogen tank under a predetermined filling control law (S2); and a determination step of determining whether a measurement error parameter corresponding to a difference between a filling amount of hydrogen gas calculated using information transmitted from the vehicle side and a filling amount of hydrogen gas calculated using a mass flow meter is within a predetermined permissible range (S9). In the filling step, the filling control law is changed after starting the filling of hydrogen gas, according to a determination result obtained in the determination step (S13 and S16).