The morphology evolution mechanism and dynamics of Cu6Sn5 intermetallic compound (IMC) in cooling stage were studied by using pure Sn solder ball with a diameter of 1 mm to react with polycrystalline Cu substrate and form Cu6Sn5. A nearly uniform height of the scallop-like IMC grains is attained by using high pressurized air to remove excess liquid solder (that is, for acquisition of the IMC morphology identical to heat preservation stage). But the morphology evolution of IMC in the solder joint was greatly affected by the cooling phase of interfacial reaction, and IMC morphology partition phenomenon was found in the spherical joints. The IMC at the edge portion characterized scallop morphology whereas the central portion possessed prismatic shape morphology. Finite element simulation for the temperature field distribution in the solder ball-substrate domain showed temperature gradient in solder’s internal core was significantly greater than that at the edge. Using this simulation results with kinetic equations, it could be understood that the central core region is conducive to the formation of small plane structure morphology. These small planes would eventually form the prismatic morphology IMC in the central region. As the soldering temperature increases, the area ratio of IMC with scallop-like morphology to the prismatic shaped IMC reduced from 0.2178 down to 0.1680. Moreover, for an elevated temperature of 300 °C, it is observed that the central region IMC (with prismatic structure) grows upto an average thickness of 7.7245 μm, whereas the thickness value for scalloped IMC at the edge portion is around 4.556 μm.