Micro-shot peening on AISI 304 and 316 stainless steel (SS) laser welds was performed to evaluate its effect on the susceptibility to stress corrosion cracking (SCC) in a salt spray containing 10% NaCl at 80 °C. The cracking susceptibility of the welds was disclosed by testing U-bend specimens in a salt spray. Micro-shot peening caused an intense but narrow deformed layer with a nanocrystal structure and residual compressive stress. Austenite to martensite transformation occurred heavily on the top surface of the micro-shot peened welds. SCC microcracks were more likely to be initiated at the fusion boundary (FB) of the non-peened welds. However, fine pits were formed more easily on the micro-shot peened 304 fusion zone (FZ), which was attributed to the extensive formation of strain-induced martensite. The nanograined structure and induced residual compressive stress in the micro-shot peened layer suppressed microcrack initiation in the 304 and 316 welds in a salt spray. Compared with the other zones in the welds in a salt spray, the high local strain at the FB was the cause of the high cracking susceptibility and could be mitigated by the micro-shot peening treatment.