A high-performance liquid chromatographic method was proposed for the separation of relative impurities in industrial 3-methylflavone-8-carboxylic acid (MFCA) and its intermediate methyl 3-propionylsalicylate (MPS). Benzoic acid (BA), MPS, 6-chloro-3-methylflavone-8-carboxylic acid (MFCA-Cl) and methyl 5-chloro-3-propionylsalicylate (MPS-Cl) in MFCA, and MPS-Cl in MPS were respectively quantified by an external standard method. As results showed, the linearity of standard curves was excellent with the relative coefficients of over 0.999 for all the detected components, and the intra- and inter-day precisions of impurities determination were satisfactory with the relative standard deviation of not more than 8.0%. Under the selected experimental condition, the chromatographic fingerprints of MFCA and MPS were drawn synthetically, and the transfer of impurities in the stepwise reactions of MFCA manufacture was elucidated. The fingerprints have great potential in instructing the production of MFCA for industrial use and in conducting the conversion of relative impurities.