A gold/silicon nanocomposite structure (NCS) was formed on a Si(100) surface by nanosecond pulsed laser irradiation. The Au/Si NCS contained both Au nanoparticles (NPs) and Au-Si alloy layers. We report that the use of laser irradiation to form Au NPs comprises two competing processes: a top-down effect involving decomposition into smaller NPs and a bottom-up effect involving self-assembly or self-organization into larger NPs. The formation of the periodic structure involved self-organization, i.e., the bottom-up effect, and was observed in situ using a pulsed-laser-equipped high-voltage electron microscope. The NCS formed by laser irradiation can be controlled by adjusting the laser energy density and the number of laser pulses.