There has been an on-going pursuit for relations between the levels of chemicals in plants/crops and the source levels in soil or water in order to address impacts of toxic substances on human health and ecological quality. In this research, we applied the quasi-equilibrium partition model to analyze the relations for nonionic organic contaminants between plant/crop roots and external soil/water media. The model relates the in-situ root concentration factors of chemicals from external water into plant/crop roots (RCF(water)) with the system physicochemical parameters and the chemical quasi-equilibrium states with plant/crop roots (αpt, ≤1). With known RCF(water) values, root lipid contents (flip), and octanol-water Kow’s, the chemical-plant αpt values and their ranges of variation at given flipKow could be calculated. Because of the inherent relation between αpt and flipKow, a highly distinct correlation emerges between log RCF(water) and log flipKow (R2 = 0.825; n = 368), with the supporting data drawn from 19 disparate soil-plant studies covering some 6 orders of magnitude in flipKow and 4 orders of magnitude in RCF(water). This correlation performs far better than any relationship previously developed for predicting the contamination levels of pesticides and toxic organic chemicals in plant/crop roots for assessing risks on food safety.