With the development of earth’s critical zone, the crucial hydropedological problems are needed to be solved. The quantitative expression of preferential flow and soil structure and stratification, water flow in situ and solute transport is the key research to the earth’s critical zone. Phosphorus loss from soils and water flow has been a vital water quality issue because of the critical role that phosphorus plays in eutrophication. Preferential flow pathways (PFPs) are one of main factors that affect subsurface phosphorus transport, which are the direct connections between soil surface and groundwater. The phosphorus fractions of two types of soil, Regosols from Gongga Mountain and Stagnosol from Ore Mountain, were investigated by using the modified Hedley sequential phosphorus extraction method. Regosols in Gongga Mountain was developed by the moraine colonization by plants in the relatively mild and humid climate. PFPs were identified by the dye tracer experiments using brilliant blue FCF. The tracerinfiltration patterns were parameterized by dye coverage ratio (Dc) and evaluation index of PFPs (Cv). The impact of PFPs on the distribution of phosphorus fractions was evaluated by the Pearson correlations and T-test. The results indicated that dye coverages of Regosols from Gongga Mountain and Stagnosol from Ore Mountain were 31% and 52%, respectively. The degree of preferential flow in Ore Mountain Stagnosol soil was tended to be larger than that in Regosols soil from Gongga Mountain;PFPs in Gongga Mountain were important contributors to the potential bioavailable inorganic phosphorus (PBPi) and organic phosphorus load, while PFPs in Ore Mountain were important contributors to the readily bioavailable inorganic phosphorus (RBPi). In conclusion, the results showed that soil types could affect both the infiltration patterns of PFPs and the transfer process of phosphorus fractions.