Benzo (α) pyrene in soybean oil was determined by molecular imprinting column purification combined with high performance liquid chromatography (MIC-HPLC). The whole process was analyzed to evaluate the uncertainty of the analytical results. Meanwhile, the uncertainty components were quantified and synthesized by a metrological model of uncertainty. Furthermore, the extended uncertainty of the measurement results was calculated. The results showed that the main factors which affected the uncertainty were the calibration curve, recovery, sample weighting and working solution preparation. When the content of benzo (α) pyrene in soybean oil was 8.735 μg/kg, at 95% confidence interval, the expanded uncertainty was 0.794 μg/kg (k=2). The uncertainty of benzo (α) pyrene in edible oil determined by MIC-HPLC can be reduced by strictly control the processes of the curve fitting, recovery, sample weighting and working solution preparation.