Recognizing the structure of human well-being related to ecosystem services is an important first step to addressing the associated environmental issues. This paper aims to analyze the structure of human well-being related to ecosystem services in Japan (including coastal and inland areas). Satisfaction levels with the five components of human well-being (basic material for a good life, health, good social relations, security, and freedom of choice and action), as defined by the Millennium Ecosystem Assessment, were investigated using a questionnaire. Of the five components, structural equation modeling analysis indicated that “security” and “basic materials for a good life” functioned as explanatory variables, while “freedom of choice and action” acted as a dependent variable through its effects on the intermediate variables “health” and “good social relations”. This study obtained similar findings to previous studies regarding the structure of human well-being. The present results also indicate that the structural model of human well-being related to ecosystem services might be psychologically shared among people.