In this paper, a novel paper-based Surface enhanced Raman spectroscopy (SERS) substrate with high sensitivity, good uniformity and popular price is developed via liquid/liquid interface self-assembly technique. Three pigment, rhodamine B, sunset yellow and chrysoidine were detected through paper-based SERS substrates using a portable Raman spectrometer. The structures of the three pigments were investigated and vibrational modes of characteristic peaks of three pigments were assigned. SERS spectra of rhodamine B, sunset yellow and chrysoidine in aqueous solution with different concentrations were detected respectively. Rhodamine B, sunset yellow and chrysoidine in drinks were also detected in drinks without any pretreatment. Within a certain range of concentrations, it meets certain function. For rhodamine B and sunset yellow, the relationship between concentration and Raman peak intensity is on an index curve, while for chrysoidine, the relationship is linear. In addition, high recoveries are achieved for detecting rhodamine B, sunset yellow and chrysoidine in drinks, which indicated our method is suited for semi-quantitative analysis for the concentration of rhodamine B, sunset yellow and chrysoidine in drinks. Surface-enhanced Raman spectroscopy provides an easy approach to fast and efficient detection for multiple pigments in drinks and can be used for quality control and market monitoring of drinks.