In this study, the effects of omega-3 fatty acids on egg production, nutrients digestibility, eggs yolk lipid peroxidation, and intestinal morphology in laying hens under physiological stress were investigated. Ninety-six 35-wk-old Lohmann LSL-Lite laying hens were used in 2 × 3 factorial arrangement with 2 levels of dexamethasone (
DEX
) (0 and 1.5 mg/kg of the diet) and 3 levels of omega-3 fatty acids (0, 0.24, or 0.48% of the diet) in a completely randomized design. At 41 wk of age, the stress groups were continuously fed with a DEX 1.5 mg/kg diet for 1 wk. Egg production, egg mass, feed intake, egg weight, and feed conversion ratio were recorded. In addition, the AME, digestibility of CP, crude fat (
CF
), and organic matter were measured during the stress induction period. At the end of 41 wk of age, malondialdehyde and cholesterol concentrations in the egg yolk and intestinal morphology were investigated. The results showed that egg production, egg mass (
P
< 0.0001), egg weight (
P
= 0.043), and BW (
P
= 0.0005) were lower in DEX layers. Feed intake was reduced by the interaction between DEX and omega-3 fatty acid (
P
= 0.042). Malondialdehyde value (
P
= 0.002) and cholesterol concentration (
P
= 0.001) in egg yolk increased by DEX administration. The combination of DEX administration and omega-3 fatty acids supplementation was found in the indices of intestinal morphology such as villus height and width and crypt depth (
P
< 0.05). Administration of DEX decreased the CP digestibility (
P
< 0.0001) and AME (
P
= 0.006). Digestibility of CF and AME in the group of 0.48% omega-3 fatty acids were higher (
P
< 0.05) than those of 0 and 0.24%. In conclusion, we found that dietary omega-3 fatty acids had beneficial effects on gut morphology and nutrient digestibility in laying hens under physiological stress. However, they could not alleviate the negative effects of physiological stress on performance.