A hydrogen storage system includes: a first hydrogen tank provided in a fuel cell electric vehicle; a second hydrogen tank provided in the fuel cell electric vehicle and configured to store hydrogen independently of the first hydrogen tank; a manifold provided in the fuel cell electric vehicle and connected to the first hydrogen tank and the second hydrogen tank; a hydrogen supply line configured to connect the manifold and a fuel cell stack provided in the fuel cell electric vehicle; and a flow rate adjusting valve configured to adjust a flow rate of the hydrogen to be supplied to the manifold from at least one of the first hydrogen tank or the second hydrogen tank in accordance with a difference in pressure between the first hydrogen tank and the second hydrogen tank, so as to minimize a difference in pressure between the hydrogen tanks to improve safety and reliability.