Flexible platforms have attracted much attention in fabricating surface enhanced Raman scattering (SERS) sensor due to its enormous practical application potential. However, traditional substrates with two-dimensionality only containing metal nanostructure limit the available development. Here, we report a distinctive method to fabricate a three-dimensional (3D) flexible SERS substrate based on graphene oxide/Ag nanoparticles/pyramidal PMMA (GO/AgNPs/P-PMMA). Taking advantages of large surface area and 3D focal volume of P-PMMA, the sensitivity for low concentration of rhodamine 6G (R6G of 10(-10) M) and crystal violet (CV of 10(-9) M) is revealed. The GO, as a protective film and an excellent absorber to probe molecules, makes a great contribution to the stability of the SERS signals. In addition, the flexible substrate presents robustness in the process of shrink proved by experiment and theory, which also realizes the in-situ detection on trace malachite green (MG) solution (10(-10) M). Furthermore, the good homogeneity, repeatability and high optical transparency are confirmed in this experiment. We believe that our approach will provide a promising material platform for universally adaptable SERS substrate.