how are ions different from atoms? how are ions different from atoms? an atom has more neutrons than an ion. an atom has a higher atomic number than an ion. an atom has a neutral charge because it has an equal number of protons and electrons, whereas an ion has a positive or a negative charge. an ion has a neutral charge because it has an equal number of protons and electrons, whereas an atom has a positive or a negative charge. an ion has a higher atomic number than an atom.