Taking examples of metaphor argumentation in synthetic biology and following pragmatic argumentation theory, this study analyzes the use of metaphor in scientific argumentation. Based on an analytical reconstruction and critical evaluation of metaphorical arguments, some suggestions are proposed for how to use metaphors reasonably in scientific argumentation.In the second half of the 20th Century, with the development of metaphor research, more and more researchers began to explore metaphors in science. While acknowledging the epistemological and methodological significance of using metaphors in science, some scholars have also pointed out the possible negative impact of using metaphors in scientific research. However, these studies usually examine the meaning and impact of a single metaphorical phrase at a macro level, giving scant attention to the use of metaphors in specific scenes at a micro level, and until now there are no clarified criteria for the rationality of metaphor use in science. In fact, metaphors are often embedded in specific scientific contexts, giving rise to a complicated process of comprehension, reasoning, and transfer of ideas and emotions. In this process, the use of metaphors can have a positive or negative impact on the context. Therefore, it is meaningful to scrutinize the use of metaphors in a specific scientific scene at a micro level. As an essential part of scientific research, the use of metaphors in scientific argumentation deserves special attention.This study has sorted out the influential metaphorical expressions in synthetic biology, and selected three metaphorical arguments used in this field according to the definition of metaphorical argumentation. By removing the redundant information, adding the potential information, replacing the ambiguous expressions with the clearer ones, and reordering the statements in metaphorical arguments, we have found that using metaphors can be a necessary move in argumentation. In scientific argumentation, metaphors can be used as a material premise to provide a data basis for argumentation, as a connection premise to perform the reasoning from premise to conclusion, and also as a standpoint to show the arguer’s thinking process. However, when metaphors are used as a particular element of arguments, it is necessary to put forward certain corresponding evaluation criteria for metaphors in order to ensure the reliability of scientific argumentation. In this study we have found that when a metaphor is used as a material premise, the metaphor should be a conventional one in scientific research and should have factual authenticity in the context of argumentation, otherwise the use of metaphor is unreasonable. When a metaphor is used as a connection premise, it will produce a symptomatic relation. And the higher the similarity of factual conditions of metaphor to the attributes conveyed by its symptomatic relation is, the higher the probability of successful argument will be. And when metaphor is used as a standpoint, it is necessary to ensure that there is no challenge to the metaphor in the context of argumentation, otherwise the standpoint is unreliable.Therefore, metaphors should be used reasonably in scientific argumentation. Only when appropriately used in scientific arguments can metaphors be accepted and recognized by the scientific community and play an active role in scientific research. On the other hand, any unreasonable use of metaphors can lead to unreliable scientific argumentation, hindering the progress of scientific research.