Ordered arrays of metal nanoparticles are important for nanoelectronic and nanophotonic applications. Here, we report the formation of self-assembled arrays of gold nanoparticles on molecular layers of diacetylene compounds on a MoS2(0001) substrate. The arrangement of gold nanoparticles is observed using scanning tunneling microscopy. When gold is deposited on a self-assembled monolayer of 10,12-nonacosadiynoic acid or 10,12-octadecadiynoic acid on a MoS2(0001) substrate, the ordered array of diacetylene moieties in the molecular layer serves as a template for the formation of ordered arrays of gold nanoparticles. In contrast, when gold is deposited on a pristine MoS2(0001) surface or on a molecular layer of stearic acid, the gold nanoparticles are randomly distributed on the surface. It is found that the arrangement of gold nanoparticles is largely determined by the deposition rate; faster deposition results in more ordered arrays of gold nanoparticles. Our observations confirm the role of unsaturated pi systems in molecules acting as a template for the regular arrangement of gold nanoparticles; this work will open up new possibilities for interfacial nanoarchitectonics.