Thought control ability (TCA) plays an important role in individuals' health and happiness. Previous studies demonstrated that TCA was closely conceptually associated with happiness. However, empirical research supporting this relationship was limited. In addition, the neural basis underlying TCA and how this neural basis influences the relationship between TCA and happiness remain unexplored. In the present study, the voxel-based morphometry (VBM) method was adopted to investigate the neuroanatomical basis of TCA in 314 healthy subjects. The behavioral results revealed a significant positive association between TCA and happiness. On the neural level, there was a significant negative correlation between TCA and the gray matter density (GMD) of the bilateral amygdala. Split-half validation analysis revealed similar results, further confirming the stability of the VBM analysis findings. Furthermore, gray matter covariance network and graph theoretical analyses showed positive association between TCA and both the node degree and node strength of the amygdala. Moderation analysis revealed that the GMD of the amygdala moderated the relationship between TCA and happiness. Specifically, the positive association between TCA and self-perceived happiness was stronger in subjects with a lower GMD of the amygdala. The present study indicated the neural basis underlying the association between TCA and happiness and offered a method of improving individual well-being.