We report a simple method to fabricate two-dimensional (2D) periodic non-close-packed (ncp) arrays of colloidal microspheres with controllable lattice spacing, lattice structure, and pattern arrangement. This method combines soft lithography technique with controlled deformation of polydimethylsiloxane (PDMS) elastomer to convert 2D hexagonal close-packed (hcp) silica microsphere arrays into ncp ones. Self-assembled 2D hcp microsphere arrays were transferred onto the surface of PDMS stamps using the lift-up technique, and then their lattice spacing and lattice structure could be adjusted by solvent swelling or mechanical stretching of the PDMS stamps. Followed by a modified microcontact printing (microcp) technique, the as-prepared 2D ncp microsphere arrays were transferred onto a flat substrate coated with a thin film of poly(vinyl alcohol) (PVA). After removing the PVA film by calcination, the ncp arrays that fell on the substrate without being disturbed could be lifted up, deformed, and transferred again by another PDMS stamp; therefore, the lattice feature could be changed step by step. Combining isotropic solvent swelling and anisotropic mechanical stretching, it is possible to change hcp colloidal arrays into full dimensional ncp ones in all five 2D Bravais lattices. This deformable soft lithography-based lift-up process can also generate patterned ncp arrays of colloidal crystals, including one-dimensional (1D) microsphere arrays with designed structures. This method affords opportunities and spaces for fabrication of novel and complex structures of 1D and 2D ncp colloidal crystal arrays, and these as-prepared structures can be used as molds for colloidal lithography or prototype models for optical materials.