Organic polymer thermoelectrics (TEs) that can realize direct heat-to-electricity conversion hold great potential in flexible and wearable applications and thus are receiving tremendous attention. Constructing polymer-based nanocomposites represents an effective approach in achieving high TE performance, while current studies on the underlying mechanisms for the improvement of TE properties in aspects of interfacial nanostructures are insufficient. In this work, flexible ternary nanocomposite films with unique interfacial architectures are developed by sequential electrochemical polymerization of conducting polymers and subsequent anion treatment. The optimized interfacial architectures contribute to enhanced π electron conjugation, which facilitates interfacial charge transfer and favours large-area charge transport. The anion treatment further enables the molecular chains to arrange in a more ordered configuration, leading to improved carrier mobility. As a result, the nanocomposites exhibit high power factors of more than 500 μW mKthat outperform most of the literature-reported peer composites. The feasible interfacial architecting and anion treatment methods proposed in this study demonstrate high potential in designing high-performance TE nanocomposites.