An ion source apparatus has an ion source assembly and a neutralizer. The ion source assembly has a body, a heat-dissipating device, an anode chunk and a gas distributor. The heat-dissipating device has a thermal transfer plate and a first thermal side sheet. The thermal transfer plate has a top, a protrusion and an annular disrupting recess. The protrusion is formed at the top of the thermal transfer plate. The disrupting recess is radially formed around the protrusion. The first thermal side sheet surrounds the protrusion. The gas distributor is mounted securely in the protrusion. Because the protrusion is located between the gas distributor and the first thermal side sheet and the disrupting recess is radially formed around the protrusion, accumulated ions, molecules and deposition film particles are longitudinally disrupted and do not form a short circuit between the gas distributor and the first thermal side sheet.