To realize the simultaneous determination of silicate and phosphate, various parameters, such as maximum wavelength, concentration of ammonium molybdate, reaction temperature, reaction coil length, acidity of masking reagent, have been optimized and a flow injection spectrophotometric system was developed based on molybdenum yellow method and reaction difference rate. The system has simple and rapid testing procedure, good reproducibility, and can been used for the development of an on line phosphate and silicate analyzer. Determination ranges of the system are 0.05~30 mg/L for phosphate and 0.1~30 mg/L for silicate. Relative standard deviations for metasilicate and orthophosphate were ≤ 1.2% and 0.9%, respectively. Recovery ranges of silicate and phosphate in the samples are 98%~103%. Sampling frequency of the method is 60~120 samples/h. It has been used successfully to determine silicate and phosphate in boiler water at power plants.