A method for the determination of trace-enrofloxacin and ciprofloxacin in bean sprouts by using ultra- performance liquid chromatography-tandem mass spectrometry was established. The mathematical model was established and used to evaluate the uncertainty components of this method. The sample was extracted with 0.1% acid acetonitrile directly, and purified by prime HLB (SPE), then analyzed by UPLC-MS/MS. The results showed that the main sources of uncertainty arose from the standard curve fitting and standard solution. The expanded uncertainty was 1.5 and 2.3 μg/kg for enrofloxacin and ciprofloxacin contents of 8.6 and 11.0 μg/kg in bean sprouts (k=2), respectively.