Self‐esteem is a widely studied construct in psychology that is typically measured by the Rosenberg Self‐Esteem Scale (RSES). However, a series of cross‐sectional and longitudinal studies have suggested that a simple and widely used unidimensional factor model does not provide an adequate explanation of RSES responses due to method effects. To identify the neural correlates of the method effect, we sought to determine whether and how method effects were associated with the RSES and investigate the neural basis of these effects. Two hundred and eighty Chinese college students (130 males; mean age = 22.64 years) completed the RSES and underwent magnetic resonance imaging (MRI). Behaviorally, method effects were linked to both positively and negatively worded items in the RSES. Neurally, the right amygdala volume negatively correlated with the negative method factor, while the hippocampal volume positively correlated with the general self‐esteem factor in the RSES. The neural dissociation between the general self‐esteem factor and negative method factor suggests that there are different neural mechanisms underlying them. The amygdala is involved in modulating negative affectivity; therefore, the current study sheds light on the nature of method effects that are related to self‐report with a mix of positively and negatively worded items.