The effect of surface characteristics and morphology of poly(imide siloxane) (PIS) on the true interfacial adhesion between PIS films and alloy-42 substrates was studied. The effect of the viscosity of PIS films and the surface treatment of deep UV/O3 (d-UV/O3) on alloy-42 plates on the peel strength of PIS films/alloy-42 joints has also investigated. 3,3′,4,4′-benzophenone tetracarboxylic dianhydride/2,2′-bis[4-(3-aminophenoxy)phenyl]sulfone (BTDA/m-BAPS) based PIS films with α,ω-bis(3-aminopropyl)polydimethyl siloxane (APPS) molecular weight Mn = 996 g/mole (PIS9Siy) show two phases in all compositions and the linear dependence of the critical surface tension on the surface concentration of the silicon, [Sisurf], on the PIS films. The PIS films with the APPS Mn = 507 g/mole (PIS5Siy) or Mn = 715 g/mole (PIS7Siy) exhibit a morphology change from a homogeneous phase to an inhomogeneous phase starting at the mole ratio (y) of APPS/PIS = 2.7% and 1.1%, respectively. The curves of critical surface tension dependence on the [Sisurf] discontinue or deflect at these two compositions, respectively. The treatment of d-UV/O3 on alloy-42 plates improves the wetting on the alloy surface and promotes the peel strength between the PIS films and alloy-42 plates by a magnitude of ≥ 20%. These results show that the flowability of the same PIS films bonding at different temperatures significantly affects the bonding strength of the joints, but the flowability of different PIS films bonding at the same temperature, e.g. 400 °C, is not the key factor governing the bonding strength of the joints. The true interfacial adhesion of the PIS5Si0.6/alloy-42 joint is 80% higher than that of the unmodified BTDA/m-BAPS based polyimide film/alloy-42 joint. However, zero true interfacial adhesion is obtained between the PIS9Siy films and alloy-42 plates. The wetting kinetics experiment shows that the higher the siloxane content in the PIS, the higher the activation energy for the adhesive bonding process. Moreover, the phase sepration significantly increases the activation energy. The scanning electron micrographs of the peeled-off PIS film surfaces from the PIS/alloy-42 joints reveal the rougher surface morphology from the sample with the higher interfacial adhesion.