In this paper, flux doped with 0.05, 0.1, and 0.2 wt% Cu6Sn5 nanoparticles (NPs) were reasonably believed to affect the morphology and growth rate of the intermetallic compounds (IMC) between Cu substrate and Sn–3.0Ag–0.5Cu solder. Reflowing was performed at 250 °C, then isothermal aging was conducted at 150 °C up to 360 h. The experimental results show that the thickness of the IMC layer increased with the increment of aging time. When the aging time extended to 120 h or more, the Cu3Sn layer appeared on the side of the Cu substrate and also thickened as time increased. The additions of Cu6Sn5 NPs into the flux did not change the type of IMCs while the total thickness of the IMC changed visually. It was calculated that the corresponding growth rate constant of interfacial IMCs in solder joints with flux contained 0, 0.05, 0.1, and 0.2 wt% Cu6Sn5 NPs were 0.14766, 0.14719, 0.14578 and 0.14726 μm/h1/2, respectively. It means that adding Cu6Sn5 NPs into flux could effectively inhibit the growth of IMC layer. The strongest inhibition effect on the growth of IMC layer could be achieved when the content of Cu6Sn5 NPs was 0.1%. Flux with Cu6Sn5 NPs could also effectively inhibit the coarsening of the interfacial IMC grains, and adding 0.1% NPs to the flux has the best inhibition effect. [ABSTRACT FROM AUTHOR]