The purpose of this study was to elucidate psychological factors that may influence nausea and vomiting during pregnancy (NVP) progression in early pregnancy based on longitudinal observations. Fifty-nine pregnant women completed the Rhodes Index of Nausea, Vomiting, and Retching (RINVR) and General Health Questionnaire-28 (GHQ-28), and recorded their resting heart rate with photoplethysmography for 5 min to determine heart rate variability (HRV) indexes at 7-9 weeks and 11-13 weeks of gestation with a 4-week interval. GHQ-28 scores (total and subclasses) and HRV indexes at 7-9 weeks were compared among groups classified according to the presence of severe NVP (RINVR >/= 9 points) at the two measurement points. Among women without severe NVP at 7-9 weeks, women who developed severe NVP at 11-13 weeks had significantly higher levels of anxiety/insomnia in the GHQ-28 subclasses (p = 0.018). The cross-lagged relationship from anxiety/insomnia at 7-9 weeks to RINVR at 11-13 weeks was significant (beta = 0.367, p < 0.001). Among women with severe NVP at 7-9 weeks, women whose severe symptoms subsided at 11-13 weeks had significantly higher high-frequency (HF) power (p = 0.010), and women with relatively higher HF power demonstrated a significant reduction in RINVR (interaction effect, p = 0.035). During early pregnancy, women with strong anxiety/insomnia symptoms tend to have NVP symptoms that become more severe as the pregnancy progresses. The higher HF power in women whose severe NVP subsided within 4 weeks suggests a contribution of emotion regulation to early amelioration of NVP.