In order to passivate deep levels, hydrogen was introduced into 3C-SiC by a hydrogen plasma treatment. The effects of hydrogen were investigated by deep level transient spectroscopy (DLTS). DLTS results indicated that hydrogen passivates deep levels in the as-grown sample. However, the results also indicated that the plasma treatment simultaneously forms deep levels originated from damages in the surface region. In order to suppress the damages, we introduced a grid between the sample and the plasma source during the plasma treatment. DLTS results showed that the grid reduces the deep levels originated from the damages, retaining the hydrogen passivation effects. The defect concentration is less than 1014 cm−3 for the sample treated by the hydrogen plasma with the grid and subsequently annealed at 300 °C.