The relationship among cerebral blood flow (CBF), functional connectivity (FC), and suicidal ideation (SI) in MDD patients has been elusive. 175 participants including 47 MDD without SI (MDDNSI), 59 MDD with SI (MDDSI), and 69 controls (HC) underwent ASL, resting-state fMRI scans, and completed neuropsychological tests. Results showed that CBF was increased in MDDSI patients in the bilateral precuneus. MDDSI patients exhibited enhanced FC in the prefrontal-limbic system and decreased FC in the right precentral gyrus relative to MDDNSI patients. Mediation analyses identified that the FC could mediate the association between CBF and behavioral performance in subgroups.