The study of an ion beam transport mechanism contributes to the production of a good quality ion beam with a higher current and better beam emittance. The simulation of an ion beam provides the basis for optimizing the extraction system and the acceleration gap for the ion source. In order to extract an ion beam from an ion source, a carefully designed electrode system for the required beam energy must be used. In our case, a self-extracted penning ion source is used for ion generation, extraction and acceleration with a single accelerating gap for the production of neutrons. The characteristics of the ion beam extracted from this ion source were investigated using computer code SIMION 8.0. The ion trajectories from different locations of the plasma region were investigated. The simulation process provided a good platform for a study on optimizing the extraction and focusing system of the ion beam transported to the required target position without any losses and provided an estimation of beam emittance.