Crack-free three-dimensional (3D) colloidal silica crystals are fabricated on an elastomeric polydimethylsiloxane (PDMS) stamp via the lift-up method. A surface relief structure is fabricated on the PDMS substrate to enable the formation of colloidal crystal assemblies that cannot be achieved on a plane PDMS substrate owing to the hydrophobic nature of its surface. Four samples of uniform silica particles having different sizes are prepared for colloidal crystal assembly on PDMS substrates with various relief patterns. This strategy not only provides a means for the assembly of crack-free colloidal crystals on a soft hydrophobic surface via the lift-up method but enables the transfer of the crack-free colloidal crystals onto a curved surface.