<p>This paper takes Sn–Ag–Cu solder as the research object, and prepares samples of the intermetallic compounds (IMCs) layer at the mesoscopic scale close to the actual working conditions according to the technological process. The load–displacement curve of the intermetallic compound is obtained through the nano-indentation technique. Two types of Berkovich indenters are used to measure the mechanical property parameters such as the elastic modulus and hardness of the tiny IMCs sample layer, which can characterize the mechanical properties of this layer. Then, the finite element simulation is iterated, and the characteristic stress and characteristic strain of the two groups of IMCs layer are obtained through inverse analysis combined with the simulation results. By shielding the uncertainties of a single experiment, an accurate constitutive relationship of the IMCs layer of the intermetallic compound is obtained. Finite element simulations of solder joints in packaging structures show significant differences between this constitutive model and traditional ones, providing reliable technical support for improving the stability of packaging structures.</p>