Microspheres could be utilized in the industrial waste water treatment due to their huge specific surface areas and surficial functional groups, which possibly adsorb heavy metal ions in the industrial waste. Melamine-formaldehyde (MF) microspheres were easily prepared as mono-dispersed micro-sized particles with a smooth surface. However, these rich amine groups in MF microspheres were frequently ignored for heavy metal ions adsorption owing to coordination effects. In this paper, a rough and bumpy siloxane-modified melamine-formaldehyde (Si–MF) microsphere was prepared using a dispersion polymerization method. Based on the experimental measurement, it is found that the particle size, surface morphology and dispersion state of Si–MF microspheres were significantly influenced by dispersing agent dosages, reaction temperature and pH. And Si–MF microspheres can be degraded in low pH. Moreover, the adsorption of the metal ions (Cu2+, Pb2+ and Ni2+) by Si–MF microspheres was also measured by an Inductive Coupled Plasma (ICP) instrument. The result indicated that the Si–MF microsphere showed a high adsorption capability for metal ions, especially Pb2+ as a potential metal ion trapping agent.