Prenatal ultrasonographic detection of fetal structural anomaly may adversely affect maternal mental health throughout pregnancy, particularly in the current COVID-19 pandemic. This study aims to prospectively assess maternal stress, anxiety, and depression following ultrasonographic detection of fetal structural anomaly from diagnosis until delivery during the COVID-19 pandemic. A total of 141 pregnant women at a tertiary hospital who underwent detailed scans between 16 and 24 gestational weeks were included and categorized into the study (anomaly finding, n = 65) and comparison (normal finding, n = 76) groups. Self-administered questionnaires of 10-item Perceived Stress Scale (PSS-10) and Hospital Anxiety and Depression Scale (HADS) were used to assess maternal stress, anxiety, and depression at prior detection (T1), two-to-four weeks post-detection (T2), one-to-two weeks prior to delivery (T3), and one-to-two weeks post-delivery (T4). Repeated measures of analysis of variance (ANOVA) were conducted to assess time-, between-group, and time-group interaction effect. In general, maternal stress improved, but anxiety worsened, while depression persisted, over the time from T1 to T4. The average maternal stress and anxiety levels were significantly higher among groups with fetal anomaly. The maternal stress and anxiety level were significantly affected within one-to-two weeks post-detection of fetal structural anomaly. In conclusion, maternal mental health parameters were affected differently during the COVID-19 pandemic, with higher vulnerability of stress and anxiety among pregnant women with fetal structural anomaly particularly within one-to-two weeks post-detection.