The evolution of primary and interfacial intermetallic compounds in solder joints during electromigration (EM) significantly influences the mechanical properties and reliability of solder joints. In this work, by combining high-resolution x-ray computed tomography and finite element modeling, the 3D evolution of Cu6Sn5 in a solder joint containing a single β-Sn grain with representative orientation was revealed. It is found that the growth of primary Cu6Sn5 rods and the formations of Cu6Sn5 rods/particles within the matrix and on the anode/cathode interfaces are all heavily influenced by local Cu concentrations and Cu diffusion fluxes in β-Sn, which are controlled by the β-Sn orientation and geometry of the solder joint. The unobvious growth of some Cu6Sn5 is also attributed to the high angles between [0001]Cu6Sn5 and [001]β-Sn (>45°). The orientation relationship between β-Sn and Cu6Sn5 also contributes to the growth direction of the newly formed Cu6Sn5 rod. This study provides insight into the mechanisms of EM-induced microstructure evolutions in ball-grid-array solder joints.