The mechanical properties of electron beam additive manufacturing (EB-AM) products, such as strength and ductility, are strongly influenced by the primary arm spacing of dendritic or cellular microstructures formed during solidification. In EB-AM, epitaxial growth of columnar dendrites/cells typically occurs at the bottom of molten pool. The primary arm spacing depends on the temperature gradient, cooling rate and flow velocity at the solidification front, all of which vary significantly over time due to the movement of the melt pool along the beam scanning path. Accurately predicting the microstructural evolution in molten pool thus requires incorporating these transient effects. The phase-field (PF) method is a powerful tool for simulating dendrite/cell growth. When coupled with fluid flow simulations, such as the lattice Boltzmann (LB) method, it enables prediction of microstructural change influenced by melt convection. However, due to the high computational cost, most previous PF-LB studies has been limited to two-dimensional simulations [1], despite the necessity of three-dimensional (3D) simulations for quantitative evaluations. In this study, we develop a 3D PF-LB simulation method to investigate columnar dendrite/cell growth during directional solidification under time-varying temperature gradient, cooling rate and flow velocity in the molten pool. The simulations are accelerated using high-performance parallel computing on multiple GPUs [2]. The time-dependent thermal and flow conditions are derived from multi-physics thermal fluid simulations of beam-induced melting and solidification during EB-AM [3]. This thermal fluid simulations incorporate the Marangoni effect, recoil pressure, mushy zone permeability. Using the developed method, we evaluate in detail the effects of these transient factors on primary arm spacing by comparing the results with those from PF–LB simulations under steady-state conditions. This work contributes to a more realistic prediction of solidification microstructures in EB-AM.