Fatty liver hemorrhagic syndrome (FLHS) has a high incidence rate in laying hens, and lots of FLHS-affected meat products enter the market every year. At the same time, the meat of laying hens is an important component of the human diet. However, the impact of FLHS on meat of laying hens is unknown, which could have a negative impact on consumers. To explore the effects of FLHS on chicken breast meat, a total of 36 twenty-five-wk-old Jingfen laying hens were used in the experiment. The hens were randomly divided into Control group and Model group, with 6 replicates per group and 3 hens per replicate. All chickens were raised in double-story step cages with individual pens. After a 3-wk acclimation period, the formal experiment began at 28 wk of age and lasted for 8 wk. Blood, liver, and breast meat samples were collected for the study of FLHS effects on breast meat. The impact of FLHS on meat quality was assessed by measuring indicators such as water-holding capacity and tenderness of the breast meat. Absolute quantitative lipidomics was employed to reveal the impact of FLHS on the lipid composition of chicken breast meat, and then validated by using RT-qPCR. Moreover, the volatilomics was utilized to detect changes in volatile organic compounds (VOCs) in chicken breast meat and to elucidate the resulting flavor changes. This research results showed that the meat quality of chicken breast meat decreased under FLHS, mainly manifested as reduced water holding capacity and decreased tenderness. The lipid content in the breast meat of FLHS-affected hens was significantly increased (P < 0.05). Among the affected lipids, 38 triglycerides exhibited notable elevation, possibly linked to heightened gene expression, such as lysophosphatidylcholine acyltransferase 3. The breast meat of laying hens with FLHS demonstrated an increased presence of VOCs, with 20 differential VOCs identified. Notably, 14 VOCs, particularly in 2-Undecenal, trans-Geranylacetone and ethyl nonanoate, exhibited substantial increases. These 3 VOCs had been identified as playing an important role in the formation of flavor in the breast meat of FLHS-affected laying hens. Correlation analysis suggested that the increase in these 3 VOCs might be related to the increase in lipid molecules such as phosphatidylethanolamine (38;3e) and acyl carnitine (10:3). In summary, FLHS reduced the breast meat quality of laying hens, altered its lipid profiles, and enhanced its flavor. These findings underscore the profound impact of FLHS on lipid and VOC profiles in chicken breast meat, offering valuable insights for chicken meat quality affected by FLHS.