Recently, we presented a new numerical scheme for vortex lattice formation in a rotating Bose–Einstein condensate (BEC) using smoothed particle hydrodynamics (SPH) with an explicit time-integrating scheme; our SPH scheme could reproduce the vortex lattices and their formation processes in rotating quasi-two-dimensional (2D) BECs trapped in a 2D harmonic potential. In this study, we have successfully demonstrated a simulation of rotating 3D BECs trapped in a 3D harmonic potential forming ‘cigar-shaped’ condensates. We have found that our scheme can reproduce the following typical behaviors of rotating 3D BECs observed in the literature: (i) the characteristic shape of the lattice formed in the cross-section at the origin and its formation process, (ii) the stable existence of vortex lines along the vertical axis after reaching the steady state, (iii) a ‘cookie-cutter’ shape, with a similar lattice shape observed wherever we cut the condensate in a certain range in the vertical direction, (iv) the bending of vortex lines when approaching the inner edges of the condensate, and (v) the formation of vortex lattices by vortices entering from outside the condensate. Therefore, we further validated our scheme by simulating rotating 3D BECs.