The formation and morphology of microscopic droplets on a chemically modified surface are important for many droplet-related applications. In this study, we examined the formation and morphological characteristics of nanodroplets produced in the same process of solvent exchange on a gold surface coated with a methyl-terminated alkanethiol monolayer. From atomic force microscopy images, we obtained the contact angles of polymerized nanodroplets in 12 combinations of the length of a straight alkyl chain and the type of droplet liquid. Our results show a significant decrease in the number density of the droplets as the number of methyl groups extends from 8 to 12 or 14. The contact angle of the droplets on octanethiol is significantly larger than that on dodecanethiol or tetradecanethiol, possibly because of the screening effect from the monolayer. Our results demonstrate that under the same solution conditions the morphology of surface nanodroplets is sensitive to the detailed molecular structures of the monolayer on the substrate. This finding has important implications for understanding static wetting on the microscopic scale and the origin of three-phase contact line pinning.