We demonstrated a flip-chip self-assembly with Cu/Sn microbump bonding using surface tension of water-soluble fluxes. By using the self-assembly with the fluxes, 3-mm-square chips were aligned to hydrophilic assembly sites defined on a Si substrates in face-down bonding within approximately 2 μm alignment accuracy. The flux-assisted self-assembly can realize not only the precise chip alignment by high surface tension of the water-soluble fluxes, but also the highly reliable bump bonding with Sn solder in a sequence of self-assembly process. Here, we employed several fluxes as liquids for flip-chip self-assembly and compared the resulting alignment accuracies by changing concentrations of the fluxes. In addition, after microbump bonding, we evaluated electrical characteristics. The resulting daisy chains showed good electrical characteristics with contact resistances of 17 MΩ/bump or below without solder bridges and bonding failures.