We report the formation of self-organized nano-dots on the surface of InP(100) upon irradiating it with a 500 keV Ar⁴⁺ ion beam. The irradiation was carried out at an angle of 25° with respect to the normal at the surface with 5 different fluences ranging from 1.0 × 10¹⁵ to 1.0 × 10¹⁷ ions per cm². The morphology of the ion-irradiated surfaces was examined by atomic force microscopy (AFM) and the formation of the nano-dots on the irradiated surfaces was confirmed. The average size of the nano-dots varied from 44 ± 14 nm to 94 ± 26 nm with increasing ion fluence. As a function of the ion fluence, the variation in the average size of the nano-dots has a great correlation with the surface roughness, which changes drastically up to the ion fluence of 1.0 × 10¹⁶ ions per cm² and attains almost a saturation level for further irradiation. The roughness and the growth exponent values deduced from the scaling laws suggest that the kinetic sputtering and the large surface diffusion steps of the atoms are the primary reasons for the formation of the self-organized nanodots on the surface. X-ray photo-electron spectroscopy (XPS) studies show that the surface stoichiometry changes with the ion fluence. With irradiation, the surface becomes more indium (In)-rich owing to the preferential sputtering of the phosphorus atoms (P) and the pure metallic In nano-dots evolve at the highest ion fluence. The cross-sectional scanning electron microscopy (SEM) analysis of the sample irradiated with the highest fluence showed the absence of the nanostructuring beneath the surface. The surface morphological changes at this medium energy ion irradiation are discussed in correlation with the low and high energy experiments to shed more light on the mechanism of the well separated nano-dot formation.