Phthalate metabolites are widely present in humans and can have many adverse effects on pregnant women. To date, many studies on the effects of phthalate metabolites on the risk of gestational diabetes mellitus (GDM) have been published, but the findings of these studies are controversial. We conducted a case-control study to quantify the concentrations of seven phthalate metabolites in the serum of pregnant women and to investigate their association with the risk of GDM and blood glucose levels in pregnant women. Therefore, 201 serum samples (139 pregnant women with GDM and 62 control serum samples) were collected from Hangzhou, China, between 2011 and 2012. The results showed that mono butyl phthalate (MBP; mean = 4.08 ng/mL) was the most abundant phthalate metabolites in human serum, followed by mono (2-ethylhexyl) phthalate (MEHP; mean = 1.28 ng/mL) and mono isobutyl phthalate (MiBP; mean = 1.20 ng/mL). The other results indicated significant associations between MBP (β = 2.24, 95 % confidence interval (CI): 1.02, 5.07, P = 0.050) and MiBP (β = 1.84, 95 % CI: 1.03, 3.31, P = 0.041) concentrations in human serum and the incidence of GDM. Moreover, serum MBP (β = 0.40, 95 % CI: 0.10, 0.70, P = 0.010) and MiBP levels (β = 0.18, 95 % CI: 0.010, 0.35, P = 0.047) in humans were positively associated with 2-hour blood glucose levels. Our study provides affirmative evidence on previously inconsistent findings that MBP and MiBP exposure may increase the risk of GDM in pregnant women.