Montmorillonite modified with cetyltrimethyl ammonium bromide (CTAB-SMF) and 3-mercapto propyl trimethoxy silane (TMSP-SMF) have been proven to adsorb much naphthalene in batch experiments, but their effects in soils have not been tested. In this study, 2.5% of CTAB-SMF or TMSP-SMF were added as soil amendments in phenanthrene and pyrene contaminated soils, and pot experiments with Amaranthus tricolor L. were conducted. The results showed that the addition of two amendments had no significant change on soil pH values (P>0.05), but the treated soils permeability decreased by 24.62% ±1.26% and their relative abundance of Proteobacteria and Actinomycetes in soil increased obviously compared with the control group. It was also found that the addition of two organoclays could reduce the bioavailability of PAHs in soil and the accumulation of phenanthrene and pyrene in plants. Compared with the control, the concentrations of phenanthrene and pyrene in Amaranthus tricolor L. shoots reduced by 20.1% ±9.5% and 13.9% ±16.9% with addition of 2.5% TMSP-SMF, while their concentrations in roots decreased by 16.7% ±6.6% and 21.2% ±13.3%, respectively. For CTAB-SMF, the concentrations of phenanthrene and pyrene in shoots decreased by 47.0% ±8.7% and 44.3% ±7.0%, and that in roots decreased by 59.1% ±4.7% and 60.0% ±8.1%, respectively. Furthermore, the oxidative stress in plant induced by PAHs was also reduced due to the addition of organoclays in polluted soils. The results of this study indicated that TMSP-SMF and CTAB-SMF could be used as remediation agents in PAHs-polluted soil, and CTAB-SMF could be more potential than TMSP-SMF in PAHs-polluted soil remediation.