A liquid chromatography analysis method of a compound containing tungstate radical and/or molybdate radical. The invention adopts the bonded stationary phase chromatographic column for separation. The mobile phase is prepared by a chromatographically pure agent and the water, the pH value of which is adjusted by the phosphate. A detector is a variable ultraviolet detector or a refractive index detector, which does the quantitative calculation in the corresponding wavelength range with an external standard method, an internal standard method or an internal addition method. The invention can directly perform the quantitative analysis to the compound containing tungstate radical and/or molybdate radical without eliminating the interference; is used for measuring the compound containing tungstate radical and/or molybdate radical in an inorganic phase, an organic phase or a homogeneous phase of the mixed solution of the inorganic phase and the organic phase; and has the advantages of simple operation, accurate results, good reproducibility and high sensitivity.