The micro-expression (ME) processing characteristics of patients with depression has been studied but has not been investigated in people with subthreshold depression. Based on this, by adopting the ecological MEs recognition paradigm, this study aimed to explore ME recognition in people with subthreshold depression. A 4 (background expression: happy, neutral, sad and fearful) × 4 (ME: happy, neutral, sad, and fearful) study was designed; two groups of participants (experimental group with subthreshold depression vs. healthy control group, 32 participants in each group) were asked to complete the ecological ME recognition task, and the corresponding accuracy (ACC) and reaction time (RT) were analyzed. Results: (1) Under different background conditions, recognizing happy MEs had the highest ACC and shortest RT. (2) There was no significant difference in the ACC and RT between experimental and control groups. (3)In different contexts, individuals with subthreshold depression tended to misjudge neutral, sad, and fearful MEs as happy, while neutral MEs were misjudged as sad and fearful. (4) The performance of individuals with subthreshold depression in the ecological ME recognition task were influenced by the type of ME; they showed highest ACC and shortest RT when recognizing happy MEs (vs. the other MEs). Conclusions: (1) The performance of individuals’ ecological ME recognition were influenced by the background expression, and this embodied the need for ecological ME recognition. (2) Individuals with subthreshold depression showed normal ecological ME recognition ability. (3) In terms of misjudgment, individuals with subthreshold depression showed both positive and negative bias, when completing the ecological ME recognition task. (4) Compared with the other MEs, happy MEs showed an advantage recognition effect for individuals with subthreshold depression who completed the ecological ME recognition task.