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Wire bonding is the most popular first-level interconnection technology used in traditional electronic packaging. However, fundamental research on wire-substrate material pairs will improve the quality and reliability of wire-bonded products. This chapter investigated the formation and breakage mechanism of microwelds in typical wire bonding material pairs using molecular dynamics simulations. The microscale contact model simulated the wire-substrate interaction during loading and unloading processes, and six wire-substrate material pairs with Cu, Ag, and Au were simulated. Microweld formation and breakage occurred at the atomic level, and the mechanism was studied by analyzing the loading force curve, total energy curve, atomic morphology, von Mises stress, and four critical displacement points. Results show that during the loading process, soft material pair (Ag-Ag) and stiff material pair (Cu-Cu) would generate of largest and smallest von Mises stress, separately. The smaller value of Z LB-HAFI (when the force between the wire and substrate equals around 70% of maximum value of attractive force between the wire and substrate, the atomic contact of the wire and substrate occurs, and the corresponding Z -coordinate of wire is defined as Z LB-HAFI ), the earlier atomic contact the between atoms of the wire and substrate occurs, which implies the material pair could be easier to be bonded. Among homogeneous material pairs (Cu-Cu, Au-Au, and Ag-Ag), the order of Z LB-HAFI value is Ag-Ag＜Au-Au＜Cu-Cu, and among heterogeneous material pairs, the order of Z LB-HAFI value is Cu-Ag＜Ag-Au＜Cu-Au. One material (like Au) from the homogeneous material pair with small Z LB-HAFI value could be used to form heterogeneous material pairs having improved bonding ability. It suggests to add an Au coating to the surface of Cu wire to reduce both bonding difficulty and high cost of using pure Au.