Voidage (porosity or void fraction) in packed particles (or pebbles) is of fundamental importance in calculating the pressure drop, obtaining the drag, predicting the bed permeability, estimating the neutron streaming, etc. For the case when particles are deformed, a method of voidage correction during the packing state is proposed using a Discrete Element Method (DEM) simulation of 3D pebble flow inside a bed of cycloidal base. A function to evaluate the remaining volume of a pebble intercepted by horizontal and vertical planes is proposed for voidage calculation. After that, the process of solving voidage distribution is provided in detail. Using this method, the voidage inside the cycloidal-base pebble bed is obtained to refer to reported similar data for validation. This method can be potentially used for dynamical voidage calculation in CFD-DEM simulation which can get suitable voidage distribution after the correction.