In bio-inspired systems, the hierarchical structures of biomolecules are mimicked to impart desired functions to self-assembled materials. However, these hierarchical architectures are based on multicomponent systems, which require not only a well defined primary structure of functional molecules but also the programming of self-assembly pathways. In this study, we investigate pathway complexity in the energy landscape of the syndiotactic poly(methyl methacrylate) (-PMMA)/C/toluene complex system, where C and toluene serve as guests in the -PMMA helical host. Structural characterization revealed that -PMMA preferentially wraps around C, forming a thermodynamically favorable helical inclusion complex (HIC). However, during the preparation of the -PMMA/C HIC, a lengthy guest-exchange pathway was discovered, where the -PMMA/toluene HIC transformed into the -PMMA/C HIC. This pathway complexity may hinder the formation of the -PMMA/C HIC within a feasible timeframe. Given that the energy landscape can be modulated by temperature, the -PMMA host can directly wrap around C in higher temperature ranges, thereby bypassing the guest-exchange process and increasing the -PMMA/C HIC formation efficiency. Additionally, after self-assembly programming, the -PMMA/C HIC can serve as an excellent photochemical reduction site. The well dispersed nanodomains of the -PMMA/C HICs act as nanoparticle templates for surface-enhanced Raman scattering (SERS) hotspot fabrication. We successfully utilized these HIC templates to synthesize self-assembled SERS-active silver nanoparticle arrays, demonstrating their potential for use in chemical sensing applications. In summary, a clear energy landscape can guide supramolecular engineering to achieve the desired supramolecular architectures by selecting appropriate self-assembly pathways.