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The optoelectronic properties of organic electronic materials are significantly affected by their molecular packing and local environments. Herein, atomic force microscopy (AFM) is used to characterize nanowhiskers of poly(3-hexylthiphene) (P3HT). The P3HT nanowhiskers form layered structures with distinctive heights that increase over time, suggesting that layered structures are more thermodynamically favored in solution. Further inspection reveals that the monolayer (ML) nanowhiskers are consistently wider than double-layered (DL) ones. The width disparity is likely due to the sliding of π–π stacked motifs within ML nanowhiskers evident by the rougher edges of ML nanowhiskers. Conversely, the interfacial interactions between two P3HT monolayers may inhibit the sliding of conjugated motifs inside the DL nanowhiskers, leading to much narrower and tightly packed structures. Kelvin probe force microscopy (KPFM) measurements are carried out to investigate the influence of ML and DL nanowhiskers’ morphologies...