We established a method to distinguish photons and neutrons in the calorimeter for the KOTO experiment which studies a rare neutral-kaon decay $K_L \to \pi^0\nu\bar{\nu}$. The method uses timing information from both front and rear ends of cesium iodide crystals used in the calorimeter. We expect that this new method, combined with the analysis techniques, will suppress the neutron background to be less than 0.2 events when the sensitivity reaches the level of Standard Model prediction.