Although thyroid dysfunction in early pregnancy may have adverse effects on pregnancy outcomes, few studies have examined the relationship between maternal low free thyroxin (FT4) levels in both first and third trimesters of pregnancy and the incidence of adverse pregnancy outcomes. We hypothesized that low FT4 levels in either first or third trimesters of pregnancy may have different effects on pregnancy outcomes. The study included 6,031 mothers who provided both first and third pregnancy serum samples for analyses of thyroid function. Adverse pregnancy outcomes, such as gestational diabetes mellitus (GDM), pregnancy-induced hypertension and preeclampsia, were diagnosed using the oral glucose tolerance test, blood pressure and urine protein test. Serum metabolites like adenosine and its analogues were identified using hydrophilic interaction liquid chromatography (HILIC)-tandem mass spectrometry (MS/MS). The incidence of hypothyroidism in pregnant women tended to increase with age and pre-pregnancy body mass index (BMI). The incidence of GDM was negatively correlated with maternal FT4 levels during early pregnancy while the incidence of preeclampsia was negatively correlated with maternal FT4 levels during late pregnancy. The incidence of pregnancy-induced hypertension was not significantly correlated with maternal FT4 levels. The women who had isolated maternal hypothyroxemia (IMH) in the third trimester of pregnancy had an increased risk of developing preeclampsia. Some metabolites like adenosine and its analogues in the serum were significantly changed in pregnant mothers with IMH. In conclusion, low FT4 levels during pregnancy are a risk factor for GDM and preeclampsia. Adenosine and its analogues may be important bridges between IMH and preeclampsia.