The high reliability of solder joints is the guarantee for the miniaturization, ultra-high density, multi-functional and high performance of integrated chips. The growth of interfacial intermetallic compounds determined by solder composition, substrates, reflow temperature et al., is the key factor to achieving good bonding. In this paper, the effects of substrate surface roughness on interfacial reaction at Sn-3.0Ag/(001)Cu interface were investigated. Confocal Laser Scanning Microscope (CLSM), Scanning electron microscope (SEM), Electron backscatter diffraction (EBSD) and Shanghai Synchrotron Radiation Facility (SSRF) were used to characterize the interface reaction. Results suggest that higher Ra favors to form thicker IMC layer and more voids, as well as degrades the preferred orientation of IM C . The results have a significant meaning in improving the reliability of solder joints in the real work environment. • The preferred orientation of Cu 6 Sn 5 can be formed on small roughness Cu single crystal substrate but it will disappear quickly. • The roughness surface is conducive to the rapid growth of IMC layer at the initial stage of reaction. • A roughness surface will result in the formation of voids at the reaction interface.