Previous studies have focused on the characteristics of ordinary facial expressions in patients with depression, and have not investigated the processing characteristics of ecological micro-expressions (MEs, i.e., MEs that presented in different background expressions) in these patients. Based on this, adopting the ecological MEs recognition paradigm, this study aimed to comparatively evaluate facial ME recognition in depressed and healthy individuals. The findings of the study are as follows: (1) background expression: the accuracy (ACC) in the neutral background condition tended to be higher than that in the fear background condition, and the reaction time (RT) in the neutral background condition was significantly longer than that in other backgrounds. The type of ME and its interaction with the type of background expression could affect participants’ ecological MEs recognition ACC and speed. Depression type: there was no significant difference between the ecological MEs recognition ACC of patients with depression and healthy individuals, but the patients’ RT was significantly longer than that of healthy individuals; and (2) patients with depression judged happy MEs that were presented against different backgrounds as neutral and judged neutral MEs that were presented against sad backgrounds as sad. The present study suggested the following: (1) ecological MEs recognition was influenced by background expressions. The ACC of happy MEs was the highest, of neutral ME moderate and of sadness and fear the lowest. The response to the happy MEs was significantly shorter than that of identifying other MEs. It is necessary to conduct research on ecological MEs recognition; (2) the speed of patients with depression in identifying ecological MEs was slower than of healthy individuals; indicating that the patients’ cognitive function was impaired; and (3) the patients with depression showed negative bias in the ecological MEs recognition task, reflecting the lack of happy ME recognition ability and the generalized identification of sad MEs in those patients.