The most common way of transportation for refined oil is long-distance pipeline. Pipeline accidents occur frequently due to corrosion, equipment failure, external forces destruction. Aiming at predicting the contaminated area in soil caused by products pipeline accidents, this experimental study was conducted to examine the relationship between the light non-aqueous phase liquids (LNAPL) accumulative infiltrate volume and the time of infiltration process in homogeneous and layered soils. The soil’s hydraulic parameters were obtained by basic experiments and RETC software. Compared with traditional infiltration mathematical model, Green-Ampt model is the most common mathematical model to calculate the infiltration process in the unsaturated soil. In this study, a modified Green-Ampt model was developed to describe water and diesel infiltration through a 100-cm-long and layered soil column. In the modified Green-Ampt model, an infiltration reduction ratio was introduced to describe the effect of the hydraulic conductivity of the layered position. To evaluate the proposed method in the effect of the layers position infiltration permeability, eight constant water head layered column infiltration experiment were conducted to record the different infiltration fluid and different constant water head infiltration process. Compared the experiment results with traditional mathematical traditional Green-Ampt model (average R2 = 0.976) and Hydrus-1D software (average R2 = 0.988) The modified Green-Ampt model had relatively higher precision in accumulative infiltrate volume (average R2 = 0.992) and the wetting front velocity in infiltration process (average R2 = 0.997). Thus, the modified mathematical model was applied an effective upscaling scheme in layered formations. The experimental result also demonstrated that soil layering affected the infiltration process. With the increase of soil depth and density, the infiltration speed of the layered soil column decreased. Additionally, the infiltrate speed of wetting front decreases slowly at the layered surface. The experiment’s fitting results showed that the modified mathematical model about infiltrate time and liquid contaminant accumulative infiltrate volume, wetting front infiltrate velocity can highly effective approach to simulate water and light non-aqueous phase liquids (LNAPL) infiltration process in layered soils.