Gallium nitride (GaN) is one of important functional materials for optoelectronics and electronics. GaN exists both in equilibrium wurtzite and metastable zinc-blende structural phases. The zinc-blende GaN has superior electronic and optical properties over wurtzite one. In this report, GaN nanodots can be fabricated by Ga metal droplets in ultra-high vacuum and then nitridation by nitrogen plasma. The size, shape, density, and crystal structure of GaN nanodots can be characterized by transmission electron microscopy. The growth parameters, such as pre-nitridation treatment on Si surface, substrate temperature, and plasma nitridation time, affect the crystal structure of GaN nanodots. Higher thermal energy could provide the driving force for the phase transformation of GaN nanodots from zinc-blende to wurtzite structures. Metastable zinc-blende GaN nanodots can be synthesized by the surface modification of Si (111) by nitrogen plasma, i.e., the pre-nitridation treatment is done at a lower growth temperature. This is because the pre-nitridation process can provide a nitrogen-terminal surface for the following Ga droplet formation and a nitrogen-rich condition for the formation of GaN nanodots during droplet epitaxy. The pre-nitridation of Si substrates, the formation of a thin SiN x layer, could inhibit the phase transformation of GaN nanodots from zinc-blende to wurtzite phases. The pre-nitridation treatment also affects the dot size, density, and surface roughness of samples.