With the advanced development of miniaturized Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS) has extended its applications into the field of point-of-care testing (POCT) and demonstrated its great significance by virtue of its noninvasive property and capability of fingerprint identification. In the SERS-based analysis and/or sensing system, the preparation of a low-cost, high-performance SERS substrate is critically important. In this manuscript, vacuum filtration is utilized to fabricate the silver nanoparticles (AgNPs)-embedded nylon filter membrane (ANFM) as flexible paper-based SERS chips. By characterizing the typical analytes with a miniaturized smartphone-based Raman analyzer, the proposed SERS chips have successfully demonstrated good sensitivity, repeatability, and stability. The lowest concentration as detected can approach 1 pmol for rhodamine 6G (RH6G) and 10 pmol for both crystal violet (CV) and malachite green (MG), respectively. With the help of the microporous structure of the membrane, the ANFM-based SERS chips can implement the separation of small molecules from a complex mixture and can achieve "purified" SERS signals of targeted molecules. Besides, with the function of antifriction resistance and flexibility, the ANFM can serve as SERS papers to preconcentrate the contaminates by multiple swapping and further enhance the SERS signals for point-of-care analysis. Therefore, we demonstrate multifunctions of the flexible ANFM-based SERS chips, which provide a promising solution for the POCT analysis with the SERS technique on account of their flexibility and low fabrication cost.