Subthreshold depression (StD) is associated with higher risk of later developing major depressive disorder (MDD). Deficits of goal-directed behaviors regarding the motional, motivational, and conflict control are found in MDD. The current study examined neural underpinning of conflict control against monetary punishment in StD compared to MDD and healthy controls (HC). Seventy-one participants (HC, n = 27; StD, n = 21; MDD, n = 23) in their mid-20’s completed self-reports. Preprocessing of functional magnetic resonance imaging acquired for the Simon task against larger or smaller monetary punishment was conducted using ENIGMA HALFpipe version 1.2.1. Neural correlates of conflict control against monetary punishment that could vary with either diagnosis or PHQ-9 total score were examined using a general linear model of FSL. Simon effect was effective for reaction time and accuracy in every subgroup of diagnosis and regardless of the size of monetary punishment. Conflict control against larger monetary loss was associated with higher functional activation of left insula in StD than HC and MDD. StD showed lower functional activation of left dorsal anterior cingulate (dACC) than MDD for conflict control against larger monetary loss. For conflict control against smaller monetary loss, StD demonstrated higher functional activation of left paracentral lobule and right putamen compared to HC. Directed acyclic graphs showed directional associations from suicidal ideation, sadness, and concentration difficulty to functional activation of paracentral lobule, ventromedial prefrontal cortex (vmPFC), and thalamus for conflict control against monetary loss. Differential functional activation of insula and dACC for conflict control against larger monetary loss could be a brain phenotype of StD. Item-level depressive symptoms of suicidal ideation, sadness, and concentration difficulty could be reflected in the conflict control-related functional activation of paracentral lobule (against smaller monetary loss), vmPFC and thalamus (against larger monetary loss), respectively.