In this article, we systematically studied the self-assembly of poly(styrene-block-dimethylsiloxane) (PS-b-PDMS) on a poly(dimethylsiloxane) (PDMS) substrate with nanoscale channels. The channeled PDMS substrate was achieved by a simple replica molding method. To decrease the effect that the subsequent solvent treatments had in distorting the soft PDMS substrate, a simple UV/O3 treatment was provided before the self-assembly, resulting in a relatively stable, harder and hydrophilic silicon oxide (SiO2) layer on the channeled PDMS surface. Ultimately, the isotropic SiO2 nanopatterns with spherical and long cylindrical morphologies were successfully fabricated by the self-assembly of two kinds of PS-b-PDMS on the PDMS substrate with nanoscale channels, respectively. In particular, we demonstrated that the introduction of isotropic SiO2 patterns is an effective approach to greatly enhance anisotropic wetting rather than that of the anisotropic structure with channels.