In this work, poly(3-hexylthiophene) (P3HT) ultrathin films (P3HT-T) were prepared by spin-coating a dilute P3HT solution (in a toluene: o-dichlorobenzene (Tol:ODCB) blend with a volume ratio of 80:20) with ultrasonication and the addition of the nucleating agent bicycle [2.2.1] heptane-2,3-dicarboxylic acid disodium salt (HPN-68L) on glass, Si wafers and indium tin oxide (ITO) substrates. The electrical and mechanical properties of the P3HT-T ultrathin films were investigated, and it was found that the conductivity and crack onset strain (COS) were simultaneously improved in comparison with those of the corresponding pristine P3HT film (P3HT-0, without ultrasonication and nucleating agent) on the same substrate, regardless of what substrate was used. Moreover, the conductivity of P3HT-T ultrathin films on different substrates was similar (varying from 3.7 S·cm−1 to 4.4 S·cm−1), yet the COS increased from 97% to 138% by varying the substrate from a Si wafer to ITO. Combining grazing-incidence wide-angle X-ray diffraction (GIXRD), UV-visible (UV-Vis) spectroscopy and atomic force microscopy (AFM), we found that the solid order and crystallinity of the P3HT-T ultrathin film on the Si wafer are highest, followed by those on glass, and much lower on ITO. Finally, the surface energy and roughness of three substrates were investigated, and it was found that the polar component of the surface energy γp plays a critical role in determining the crystalline microstructures of P3HT ultrathin films on different substrates. Our work indicates that the P3HT ultrathin film can obviously improve the stretchability and simultaneously retain similar electrical performance when a suitable substrate is chosen. These findings offer a new direction for research on stretchable CP ultrathin films to facilitate future practical applications.