We investigate variations of ion flux over the ionosphere and in the plasma sheet when storm time substorms are initiated, using simultaneous observations of neutral atoms in the energy range of up to a few keV measured by the low-energy neutral atom (LENA) imager on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite, outflowing ion flux of <1 keV measured by the ion electrostatic analyzer (IESA) on board the Fast Auroral SnapshoT (FAST) satellite, and energetic (9-210 keV/e) ion flux measured by the energetic particle and ion composition (EPIC) instrument on board the Geotail satellite. We examined three storm intervals during which the IMAGE or FAST satellite was in a suitable location to observe ionospheric ion outflow and the Geotail satellite was in the plasma sheet on the nightside. The neutral atom flux observed by IMAGE/LENA in the first interval and outflowing ion flux observed by FAST/IESA in the second and third intervals indicate that storm time substorms can cause increases of lowenergy ion flux over the ionosphere by a factor of 3-50 with time delay of less than several minutes. In the plasma sheet, the flux ratio of O+/H+ is rapidly enhanced at the storm time substorms and then increased gradually or stayed at a constant level in a time scale of ∼1 h, suggesting a mass-dependent acceleration of ions at local dipolarization and a subsequent additional supply of O+ ions to the plasma sheet which have been extracted from the ionosphere at the substorms. These coordinated observations revealed that substorms have both an immediate effect and a delayed effect (i.e., two-step effect) on the ion composition in the plasma sheet.