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Micro-expressions are often embedded in a flow of expressions including both neutral and other facial expressions. However, it remains unclear whether the types of facial expressions appearing before and after the micro-expression, i.e., the emotional context, influence micro-expression recognition. To address this question, the present study used a modified METT (Micro-Expression Training Tool) paradigm that required participants to recognize the target micro-expressions presented briefly between two identical emotional faces. The results of Experiments 1 and 2 showed that negative context impaired the recognition of micro-expressions regardless of the duration of the target micro-expression. Stimulus-difference between the context and target micro-expression was accounted for in Experiment 3. Results showed that a context effect on micro-expression recognition persists even when the stimulus similarity between the context and target micro-expressions was controlled. Therefore, our results not only provided evidence for the context effect on micro-expression recognition but also suggested that the context effect might result from both the stimulus and valence differences.