Abstract Background Childhood trauma is associated with development of depression, yet a comprehensive investigation into the relationship between childhood trauma and depression severity, as well as cognitive impairment and omega-3 polyunsaturated fatty acids (n-3 PUFAs) levels remains to be fully explored. Methods A total of 97 patients undergoing first-diagnosed, drug-naïve depression and 60 healthy controls (HCs) were recruited in this study. The evaluation included the Childhood Trauma Questionnaire (CTQ), Hamilton depression scale (HAMD), Hamilton anxiety scale (HAMA), Beck depression inventory (BDI), Self-rating anxiety scale (SAS), Repeatable battery for the assessment of neuropsychological status (RBANS) scores and n-3 PUFAs levels. Results Emotional abuse (p