Background: Allergic diseases in offspring are suggested to originate from fetal life. The role of in-utero stress exposures in early childhood allergic diseases development has not been completely elucidated. We aimed to determine the effect of exposures to different kinds of maternal stressed-affective factors during pregnancy on the risk of childhood allergy during first 2 years of life. Methods: A sample of 4178 children born in 2016-2018 from the Shanghai Maternal-Child Pairs Cohort were included in this study. Indicators for maternal stressed-affective factors included life events stress at early and late pregnancy, respectively, and prenatal depression and anxiety at late pregnancy, which were measured by the Life Events Scale for Pregnant Women (LESPW), Self-Rating Anxiety Scale (SAS) and Center for Epidemiologic Studies, Depression Scale (CES-D). The children’s allergic diseases or manifestations were assessed through the questionnaires at 2,6,12,24 months after birth, respectively, including eczema, atopic dermatitis, food allergy, wheezing, asthma, and allergic rhinitis. The impacts of maternal stressed-affective factors on child allergic diseases were analyzed using multivariable binary logistic regression adjusting for potential covariates. Results: During the first 2 years of life, all forms of allergic disease were continuously reported, with allergic diseases of skin preceded the development of other atopic diseases. Children whose mothers had high life events stress during the early pregnancy or the late pregnancy would have an increased risk of eczema at 2 months respectively (AdjOR:1.30, 95%CI:1.01-1.67; AdjOR:1.64, 95%CI:1.14-2.36). Children whose mothers with high life events stress in late pregnancy were also more likely to have food allergy at 6 months (AdjOR:3.22, 95%CI:1.27-8.12). Maternal prenatal anxiety may lead to offspring’s childhood wheeze at 24 months (AdjOR:2.15, 95%CI:1.09-4.27). Conclusions: Maternal stressed-affective factors could have effects on offspring’s allergic diseases, especially eczema at 2 months. Understanding the temporal-specific effects of maternal stressed-affective factors may better inform prevention strategies.