Baicalin is the main indicator for qualitative and quantitative analysis of Scutellaria baicalensis Georgi and its prescription in vivo and in vitro. Owing to its insolubility and instability, the analysis of baicalin in biological samples is analytically challenging. Although there have been many pharmacokinetic or metabolism studies on baicalin, the current reported sample pretreatment methods are not the optimal choice with regard to absolute recovery and operation procedure. Here we report a high-throughput salting-out-assisted homogeneous liquid-liquid extraction method with acetonitrile and ammonium sulfate. Eight kinds of commonly used salts, preferred salt concentration and auxiliary solvents were investigated. The extraction efficiency in the presence of ammonium salt and auxiliary solvent (methanol) in comparison to that from the salt-free aqueous increased to above 90%. The performance of the developed pretreatment method was further evaluated through testing specificity, linearity, precision, accuracy, extraction recovery and stability. In particular, the stability investigation results proved that the operation at low temperature would no longer necessary be for salting-out-assisted homogeneous liquid-liquid extraction compared with protein precipitation, and the pretreatment method would be valuable if the compounds were unstable within matrices.