As thiocyanate (SCN(-)) acts as an important biomarker in human health assessment, there remains an urgent need to realize rapid and reproducible analysis of SCN(-) in body fluids. Here, a droplet microfluidic device has been designed and fabricated for SCN(-) detection in real human serum and saliva using the surface enhanced Raman scattering (SERS) technique. Only a few minutes are needed for the whole detection process which simply cost a few microliters of real sample. Gold@silver core-shell nanorods (Au@Ag NRs) with a large SERS enhancement factor were selected to capture SCN(-) ions in body fluids. The intensity of SERS peak at around 2100 cm(-1), which originates from the -C≡N stretching mode, was used to indicate the concentrations of SCN(-) ions. Importantly, by generating a droplet environment for mixing reagents and acquiring signals, this microfluidic platform possesses the advantages of an improved reproducibility and reduced time consumption. For practical applications, the SERS-microfluidic system is capable to achieve rapid analysis of SCN(-) in the presence of human serum, which is very important for realizing the detection in real biological samples. Additionally, SCN(-) in saliva samples was detected in the SERS-microfluidic chip and the results provide useful information for distinguishing between smokers and nonsmokers.