In this work, the stress corrosion cracking (SCC) behavior of E690 steel base metal (BM) and different heat-affected zone (HAZ) microstructures, i.e., coarse grain HAZ (CGHAZ), fine grain HAZ (FGHAZ), and intercritical HAZ (ICHAZ), was investigated at different cathodic potentials in artificial seawater by slow strain rate tensile tests, scanning electron microscopy and electron back-scattered diffraction measurements. The results show that the HAZ microstructures and BM exhibit different SCC susceptibilities: FGHAZ < ICHAZ < BM < CGHAZ, which are controlled by anodic dissolution (AD) at the open circuit potential. With the cathodic potential equaling to −750 mV, the SCC susceptibility of the four microstructures increases because of the synergistic effect of AD and weak hydrogen embrittlement (HE). At -850 mV, AD is inhibited, and the SCC susceptibility of BM decreases, while the SCC susceptibility of the HAZ microstructures increases. At a potential below -850 mV, the SCC susceptibility of the four microstructures gradually increases because of the augment of HE, and the SCC susceptibility of the HAZ microstructures is higher than that of BM. The distinction reveals that the HAZ microstructures have the greater HE susceptibility than BM.