Abstract Background Previous studies have stressed the importance of tobacco exposure for the mood disorders of depression and anxiety. Although a few studies have focused on perinatal women, none have specifically considered the effects of smoking and secondhand smoke exposure on perinatal suicidal ideation. Thus, this study aimed to investigate the relationships of smoking/secondhand smoke exposure status with suicidal ideation, depression, and anxiety from the first trimester to the first month post partum. Methods This cross-sectional study based on self-reported data was conducted at five hospitals in Taipei, Taiwan from July 2011 to June 2014. The questionnaire inquired about women’s pregnancy history, sociodemographic information, and pre-pregnancy smoking and secondhand smoke exposure status, and assessed their suicidal ideation, depression, and anxiety symptoms. Logistic regression models were used for analysis. Results In the 3867 women in the study, secondhand smoke exposure was positively associated with perinatal depression and suicidal ideation. Compared with women without perinatal secondhand smoke exposure, women exposed to secondhand smoke independently exhibited higher risks for suicidal ideation during the second trimester (odds ratio (OR) = 7.63; 95 % confidence interval (CI) = 3.25–17.93) and third trimester (OR = 4.03; 95 % CI = 1.76–9.23). Women exposed to secondhand smoke had an increased risk of depression, especially those aged 26–35 years (OR = 1.71; 95 % CI = 1.27–2.29). Conclusions Secondhand smoke exposure also considerably contributes to adverse mental health for women in perinatal periods, especially for the severe outcome of suicidal ideation. Our results strongly support the importance of propagating smoke-free environments to protect the health of perinatal women.