Background <p>Although abnormal amygdala functional connectivity (FC) has been reported in schizophrenia, most studies have treated the amygdala as a single structure. This study aimed to explore the association between amygdala subregional FC and anhedonia in patients with first-episode schizophrenia (FES).</p> Methods <p>Resting-state functional magnetic resonance imaging (fMRI) was conducted in 31 FES patients (including 11 drug-naïve) and 33 matched healthy controls (HCs). Clinical symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS), and anhedonia was evaluated via the Snaith-Hamilton Pleasure Scale (SHAPS). Whole-brain FC analyses of amygdala subregions were performed, followed by group comparisons and correlation analyses with anhedonia scores.</p> Result <p>Compared to HCs, FES patients showed significantly reduced FC between specific amygdala subregions and cortical regions, particularly within the frontal, temporal, parietal, and limbic lobes (<i>P</i> &lt; 0.05, GRF correction). Anhedonia severity was positively correlated with altered FC in the centromedial (CM) subregion of the amygdala (AMY_CM), especially with the supplementary motor area (SMA) and paracentral lobule (PLG). Notably, the association between right AMY_CM and right SMA FC and anhedonia remained significant after adjusting for clinical symptom severity (<i>r</i> = 0.46, <i>P</i> = 0.02).</p> Conclusions <p>FES patients exhibit disrupted FC between amygdala subregions and cortical areas, with specific patterns linked to anhedonia. These findings suggest that anhedonia may be associated with a potential neurobiological marker independent of general clinical symptoms and may be indicative of amygdala–cortical dysconnectivity in schizophrenia.</p> Trial registration <p>Data used for this analysis came from case-control studies. Clinical trial number: not applicable. (April 2018 through March 2021).</p>