The heterogeneous metal nanostructures have attracted great interest in various applications due to the synergistic effects between two noble metals, especially in surface enhanced Raman scattering (SERS) region. Herein, we prepared a 3D SERS active substrate based on heterogeneous and cross-distributed metal structure hybridized with MoS2by in situ synthesizing gold nanoparticles (AuNPs) on MoS2 membrane. The AuNPs-AgNPs/MoS2/P-Si hybrid SERS substrate were characterized by a scanning electron microscope (SEM), a transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS) to investigate the character and the content of elements. In virtue of the heterogeneous and cross-distributed structure and ultra-narrow interparticle gap generating strong electric fields enhancement, the ultra-low concentration of probe molecule were detected (the LOD of 10-12 M for R6G and CV, 10-11 M for MG), serving the optimal SERS performance. The excellent uniformity and reproducibility were achieved by the proposed substrate. Moreover, the flexible MoS2/AuNPs-AgNPs/PMMA pyramidal SERS substrate was applied to detect melamine molecule in liquid milk (the LOD reached 10-9 M), which revealed great potential to be an outstanding SERS substrate for biological and chemical detection.