High-throughput laser printing of resonant silicon nanoparticles has emerged as a novel tool for the fabrication of deeply subwavelength objects with various functionalities. The applications of resonant silicon nanoparticles crucially depend on their crystalline state. However, the ways to control the crystalline structure during laser printing remain unstudied. Here we demonstrate, both experimentally and theoretically, how the crystalline structure of silicon nanoparticles fabricated by a laser printing technique can be varied from almost amorphous to a polycrystalline state. In particular, we propose a method of crystalline structure control via changing the distance between the irradiated silicon film and the receiving substrate. This study allows the most optimal conditions for second harmonic generation to be revealed. We believe that the proposed method opens the door to fully controllable laser printing of functional nanoparticles and nanostructures.