The effects of mild iodine deficiency during the first and second trimesters on both pregnant women themselves and their offspring exhibited in consistent patterns. In this study, we aimed to address this issue by employing small molecule metabolomics. A total of 98 pregnant women in either the first or second trimester were recruited, with comprehensive data including basic information, 24-hour urine samples and blood samples collected, and subsequent evaluation of birth outcomes for their offspring. The 24-hour urinary iodine excretion (UIE) was detected and used as the dividing criterion to determine the iodine nutrition status of pregnant women. Serum metabolomics assay was performed by Ultra High Performance Liquid Chromatography Orbitrap Exploris Mass Spectrometry (UHPLC-OE-MS) platform. Differential metabolites as the potential iodine deficiency biomarkers were selected by multivariate statistical analysis methods. Association analysis was used to further analyze the relationship between the potential biomarkers and neonatal birth outcomes. As a result, there was no significant difference in maternal thyroid function indicators and neonatal outcomes between mild iodine deficiency and iodine adequate pregnant women. However, the metabolic profile of pregnant women with mild iodine deficiency was significantly disturbed compare to these with iodine adequate. A total of 28 different metabolites were screened, which could be used as the potential biomarkers of iodine deficiency. After adjusted age and pregnancy trimester, the expression of these biomarkers were also changed significantly. Furthermore, these markers were also related to fatty acid biosynthesis, tyrosine metabolism, tryptophan metabolism, arachidonic acid metabolism, and pentose and glucuronate interconversions. In addition, among these markers, 2-(4-Methyl-5-thiazolyl)ethyl octanoate was found to be associated with neonatal TSH, ACar(12:0), (9S,10E,12Z,15Z)-9-Hydroxy-10,12,15-octadecatrienoic acid showed a correlation with body length; whereas (9S,10E,12Z,15Z)-9-Hydroxy-10,12,15-octadecatrienoic acid was linked to body weight. In conclusion, mild iodine deficiency during the first and second trimesters dose not result in overt adverse effects on pregnant women and their offspring. However, at the metabolic level, mild iodine deficiency may disrupt the metabolic profile of pregnant women and impact the development of their offspring.