The accumulation and spatial distribution of economically important petroleum in sedimentary basins are primarily controlled by its migration from source rocks through permeable carrier beds to reservoirs. Tracing petroleum migration entails the use of molecular indices established according to sorption capacities of polar molecules in migrating petroleum. However, little is known about molecular sorption capacities in natural migration systems, rendering these indices unreliable. Here, we present a new approach based on a novel concept of relative sorption coefficient for quantitatively assessing sorption capacities of polar molecules during natural petroleum migration. Using this approach, we discovered previously unrecognized "stripping" and "impeding" effects that significantly reduce the sorption capacities of polar compounds. These discoveries provide new insights into the behaviors of polar compounds and can easily explain why traditional molecular indices yield incorrect information about petroleum migration. In light of these new findings, we established new molecular indices for tracing petroleum migration. We demonstrate via case studies that the newly established indices, unlike traditional molecular indices, are reliable and effective in tracing petroleum migration. Our approach can be applied to diverse basins around the world to reveal distribution patterns of petroleum, which would decrease environmental risks of exploration by reducing unsuccessful wells.