The combination of plasmonic metals and photonic crystal (PC) structure is considered to have potential for further enhancement of the surface-enhanced Raman scattering (SERS) effect in comparison with conventional metal SERS substrates. Many studies have suggested that SERS signals probably suffer from an often-neglected effect of strong surface plasmon resonance (SPR)-induced photothermal heating during SERS detection. Herein, we have discovered that the photothermal heating problem arises in a traditional hybrid substrate that is prepared by doping plasmonic Au nanoparticles (NPs) into the voids of an opal PC (Au-PC). This happens mainly because excess Au agglomerates formed by non-uniformly distributed Au NPs can cause a strong SPR effect under laser illumination. To fully address this issue, we have employed an improved hybrid substrate that is fabricated by substituting Au NPs in Au-PC with an Au-loaded magnetic framework (AuMF). The AuMF can effectively prevent the aggregation of Au NPs and ensure sufficient hot spots for SERS. This novel substrate prepared by doping AuMFs into a PC (AuMF-PC) was free of strong photothermal heating and showed high SERS intensity and reproducibility of the SERS signal compared with Au-PC. For practical applications, we have demonstrated AuMF-PC as an appropriate candidate for the SERS assay of the trace thiol pesticide thiram, and it enables recycling and reuse to achieve low cost.