The purpose of the present study was to assess the effects of social capital on mental health among the Japanese population with or without natural disaster experience. A nationwide cross-sectional study was performed in the population aged 15 to 79 years old. We collected data on psychological status, social capital, disaster experience in ten years prior to the survey, and socio-demographic information. We assessed cognitive social capital (perceptions of support, reciprocity and trust), social support (support from individuals in the community), and social participation (participation in social activities) as components of social capital. The study outcome was mild mood or anxiety disorder (hereafter mood/anxiety disorder), defined as the score of 5 or higher in the Kessler Psychological Distress Scale (K6). Using logistic regression models, we tested whether each component of social capital was associated with mood/anxiety disorder with or without disaster experience. Out of 1,200 participants, 1,183 had available K6 score data and were considered. Among three components of social capital, only social support significantly interacted with disaster experience (p = 0.019). In the population without disaster experience, those with high social support were less likely to have mood/anxiety disorder (OR 0.45, 95% Cl 0.28-0.73); however, no such association was observed among those with disaster experience (OR 1.11, 95% CI 0.64-1.90). Thus, the protective effects of social support against mood/anxiety disorder vary in the Japanese population depending on disaster experience. The present study provides important insight into the role of social capital on mental health after natural disaster.