After adsorption of phenanthrene by the natural soil under different concentrations initially added, the soil sample was extracted for humic acid fraction (including humic acid and fulvic acid), and the sorption amount of phenanthrene in humin fraction was calculated to investigate the adsorption/distribution kinetics in two soil organic fractions and the corresponding influence of original phenanthrene concentration. The experimental data were fitted using Freundlich equation. The results show that, distribution of phenanthrene in the soil exhibited a multi-stage property, i.e., from a first fast sorption to a breakthrough at about 48 h, then followed by a slow sorption procedure. In the fast sorption stage (before 48 h), there was an up-to-down fluctuation of phenanthrene sorption ratio (sorption amount/added amount) in humic acid fraction, possibly due to surface sorption by minerals and competitive sorption by humin fraction. In the slow sorption stage, variations in sorption ratio in humic acid fraction was very small, and the influence of original concentration of phenanthrene was slight; while for humin fraction, the sorption ratio of phenanthrene at lower initial concentration was significantly higher than at higher one, in addition, the sorption ratio showed a gradually increasing trend, indicated humin fraction as the main domain in charge of the slow sorption. The fitting results of model parameters demonstrated that, sorption nonlinearity of phenanthrene in the natural soil increased in the following order: humic acid fraction< whole soil< humin fraction, and enhanced gradually. Different characteristics of humic acid and humin fractions in the multi-stage kinetics of phenanthrene sorption/distribution further reflected the effects of heterogenerity of soil organic fractions on nonlinear sorption behaviors.