Although there is substantial information about the effects of social relationships on mental health, their effects on postnatal bonding remain unclear. We aimed to examine the association between social isolation and postnatal bonding disorder. We analyzed data from 17,999 women who participated in the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study. An abbreviated version of the Lubben Social Network Scale was used to assess social isolation in the second trimester of pregnancy, and its subscales were used to assess marginal family ties and marginal friendship ties. Bonding disorder was defined as a Mother-to-Infant Bonding Scale score of ≥ 5 1month after delivery. Multiple logistic regression analyses were conducted to examine the association between social isolation and postnatal bonding disorder after adjusting for age at delivery, parity, feelings towards pregnancy, psychological distress during pregnancy, and household income. Analyses stratified by postnatal depressive symptoms (PDS) were also conducted. Social isolation was associated with postnatal bonding disorder: the odds ratio (OR) was 1.55 (95% confidence interval [CI], 1.41-1.71). Marginal family ties and friendship ties were associated with postnatal bonding disorder: the ORs were 1.40 (95% CI, 1.23-1.60) and 1.44 (95% CI, 1.32-1.57), respectively. Marginal family ties were associated with postnatal bonding disorder only among women without PDS: the ORs were 1.30 (95% CI, 1.10-1.55) among women without PDS and 1.13 (95% CI, 0.91-1.40) among women with PDS. Social isolation during pregnancy was associated with an increased risk of postnatal bonding disorder.