The growth of indium and aluminum nanostructures on molybdenum disulphide (MoS2)(0001) substrate has been studied using scanning tunneling microscopy in ultra-high vacuum. At low coverage and room temperature (RT), mostly ultra-thin (approximately 1.2-2 nm) triangular In islands were observed on MoS2. With increasing coverage or high flux, large coalesced irregular islands along with triangular and round-shaped ones of increased average height were found. Triangular and round-shaped islands were obtained after annealing the RT-deposited In on MoS2 sample at 450 K. At approximately 375 K, exclusively triangular In islands were observed. Al nanoparticles with diameter in 4-16 nm range were obtained after a low-flux deposited whereas ramified islands were observed in a high flux at RT. Ultra-thin (approximately 1.20-2 nm) Al islands and films were obtained on MoS2 after deposition at 500 K. These results demonstrate that the shape of In and Al nanostructures grown on MoS2 can be controlled in self-assembly by adjusting substrate temperature, deposition flux and amount.