The origin of supermassive black holes (with > 109 Msun) in the early universe (redshift z ~ 7) remains poorly understood. Gravitational collapse of a massive primordial gas cloud is a promising initial process, but there are some theoretical difficulties including the angular momentum barrier. Using a set of three-dimensional magnetohydrodynamic (MHD) simulations, we investigate the star formation process in magnetized atomic-cooling gas clouds with different initial magnetic field strengths. Our simulations show that the primordial magnetic seed field can be quickly amplified during the early accretion phase after the first protostar formation.The strong magnetic field efficiently extracts angular momentum from accreting gas and increases the accretion rate, which results in a high fragmentation rate in the gravitationally unstable disk region. On the other hand, the coalescence rate of fragments is also enhanced by the angular momentum transfer due to the magnetic effects. Almost all the fragments coalesce to the primary star. We conclude that the magnetic effects support the direct collapse scenario of supermassive star formation.