Electromagnetic ion cyclotron (EMIC) waves generated by hot anisotropic (T⊥ > T∥) protons (∼10–100 keV), play an important role in accelerating cold (<1 eV) protons (H+) and helium (He+) ions in the magnetosphere. Using a hybrid code with parameters found in the inner magnetosphere, we examine when and how cold H+ and He+ ions are energized by EMIC waves. Hybrid simulations show that the energization of the cold particles occurs in two steps. In the first step, EMIC waves, which are linearly excited in the early stage of the simulation, interact with cold H+ and He+ ions, resulting in energization mostly in the direction perpendicular to the background magnetic field. The energization in this step is mainly contributed by enhanced bulk motion of these ions as a result of the linear response, consistent with recent observations in the inner magnetosphere. In the second step, nonlinear evolution of energized cold H+ and He+ ions are confirmed in the parallel direction, which is seen after about 200 proton gyroperiods (∼8.5 s). Throughout the simulation run, cold He+ ions are much more energized in the perpendicular direction than in the parallel direction. However, the cold protons are more energized in the parallel direction than in the perpendicular direction after 500 proton gyroperiods (∼21.3 s). By comparing recent observations and the present simulation results, we suggest that the cold particle energization by EMIC waves occurs at an early stage of wave generation when the nonlinear evolution of EMIC waves is not dominant in the inner magnetosphere.