Self-relevant concepts are major building blocks of spontaneous thought, and their dynamics in a natural stream of thought are likely to reveal one’s internal states that are important for mental health. Here, we conducted a functional magnetic resonance imaging experiment ( n = 62) to examine brain representations and dynamics of self-generated concepts in the context of spontaneous thought using a newly developed free association–based thought sampling task. The dynamics of conceptual associations were predictive of individual differences in general negative affectivity, replicating across multiple datasets ( n = 196). Reflecting on self-generated concepts strongly engaged brain regions linked to autobiographical memory, conceptual processes, emotion, and autonomic regulation, including the medial prefrontal and medial temporal subcortical structures. Multivariate pattern–based predictive modeling revealed that the neural representations of valence became more person-specific as the level of perceived self-relevance increased. Overall, this study sheds light on how self-generated concepts in spontaneous thought construct inner affective states and idiosyncrasies.