The authors previously developed a new fabrication method for a metal nanodot array, by combination of nanogroove grid patterning and thermal dewetting of metal deposited on a substrate. However, a comprehensive understanding of the thermal dewetting mechanism is necessary to improve the quality and control the variation of the metallic nanodot array. In this study, thermal dewetting-induced nanodot agglomeration mechanism is studied from a theoretical point of view. An analytical model is proposed, based on the total free energy of a dot and substrate system. The theoretical minimum and natural dot sizes show the same trend with an increase of contact angle. The theoretical model is validated by the experimental results.