A structure composed of various Cu-Ni-Sn IMCs would develop from severe Joule heat and excessive elemental diffusion under high-density current in the solder joints of flexible printed circuit (FPC). Herein, we firstly observed the evolution of a Cu6Sn5 + Cu3Sn/(Ni,Cu)3Sn4 hybrid structure in a mu-Cu/NiAu/Sn/Cu solder joint for full intermetallic compounds (IMCs) interconnect of flexible electronics under isothermal aging condition by in-situ TEM. The joint was divided into two regions, the IMC type on the right region remained unchanged with dwell time prolonging, while the ratio of Cu3Sn on the left region at various dwell times fitted the JMAK model when the kinetic parameter n picked 1.5, indicating that grain boundary diffusion was the predominant mechanism for transporting Cu atoms. The nucleation and growth of Cu3Sn grains were finished in the Cu6Sn5 layer. The nucleation of a Cu3Sn grain with a spherical cap shape was firstly captured by HRTEM, and Cu3Sn grains underwent a transformation from columnar to equiaxed when the dwell time was increased, making the morphology of Cu3Sn grains in a mu-Cu/NiAu/Sn/Cu solder joint significantly different from the situation in larger solder joints. This study is expected to provide an in-depth study of the microstructural evolution of micro Cu/NiAu/Sn/Cu solder joints under aging condition and thereby expand their application in the microelectronic industry.