Poly(3-hexylthiophene) (P3HT) is a typical conjugated polymer with rather rigid backbone due to pi-conjugation of the thiophene rings. In this work, we grew nanowhiskers of monolayer thickness from P3HTs of different molecular weights, and found that the nanowhisker widths were all similar to 16 nm as measured by transmission electron microscopy, independent of the molecular weight and much smaller than the contour lengths of the P3HT chains, indicating the presence of chain folding in the nanowhiskers. Because of the geometry constrain, the chains must fold out of the conjugation plane. An out-of-plane folding model was established based on theoretical calculation results, and its energy was found to be lower than that of the in-plane folding. These results provide new insight into polythiophene crystallization behavior and suggest that conjugated polymers are more flexible than previously perceived.