This article addresses citizens’ psychological health disparities in pandemic-stricken Japan from the perspective of positive psychology with a collective/political perspective. Our analysis of three internet surveys in 2020 and 2021 in Japan indicates most people’s well-being declined continuously during this period, while some people’s well-being increased. As previous studies of health inequality proved about physical health, the objective income/assets level has influenced psychological inequality. This paper demonstrated this relation in Japan, although it is often mentioned as an egalitarian country with comparatively better health conditions. Moreover, psychological levels and changes have been associated with biological, natural environmental, cultural, and social factors. Social factors include economic, societal-community, and political factors, such as income/assets, stratification, general trust, and fairness/justice. Accordingly, multi-dimensional disparities are related to psychological health disparity; tackling the disparities along the multi-layered strata is desirable. Furthermore, subjective perception of fairness/justice is significantly associated with the level of psychological health and mitigating its decrease. Thus, fairness and justice are found to be dynamic and protective factors against the decline of psychological health. While relatively little literature on health inequality analyzes fairness/justice philosophically, this paper highlights these together with income/assets by clarifying the significance of multi-dimensional factors: natural environmental, cultural, socioeconomic, and political.

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