Shielding from space radiation, especially galactic cosmic rays (GCRs), is a significant safety challenge for future human activities in deep space. In this study, the shielding performances of potential materials [aluminum (Al), polyethylene (PE), and carbon fiber reinforced plastic (CFRP)] were investigated using Geant4 Monte Carlo simulation considering two types of biological scale parameters, the International Commission on Radiological Protection (ICRP) quality factor (QFICRP) and the plausible biological effectiveness (RBEγacute), for GCRs. The effective dose equivalent was reduced by 50% for QFICRP and 38% for RBEγacute when shielding using 20 g/cm2 of CFRP. A spacecraft made from CFRP will have a better radiation shielding performance than conventional Al-based spacecraft. The contribution of heavy ions for QFICRP based effective dose equivalent was larger by a factor of ~ 3 compared to that for RBEγacute based effective dose equivalent. The shielding materials efficiently reduced the effective dose equivalent due to ions with QFICRP > 3.36 and RBEγacute > 2.26. QFICRP and RBEγacute have advantages and disadvantages in quantifying the dose equivalent of space radiation, and the establishment of a standard parameter specified for a mixed radiation environment occupied by protons and heavy ions is necessary for practical dose assessment in deep space.