Health-related behaviors in adolescents are an important factor of morbidity and mortality. Previous studies have found that there is a close relationship between time perspective and choice preference for health behaviors, and there are differences between individuals with different trait of time perspective. The purpose of this study was to explore the implicit preferences of healthy behavior choice among middle school students with three types of time perceptive traits: present-hedonistic, present-fatalistic and future, and the role of episodic future thinking between different time perceptive trait and implicit preferences of healthy behavior choice. In this study, we used the classic IAT test to investigate the implicit preference of healthy behavior choice in middle school students. 184 subjects (mean age: 15.43±1.18 years) were selected through clustering analysis on the score of “Zimbardo Time Perspective Scale” that classified the subjects into three groups: The present-hedonistic (n=62), the present-fatalistic (n=61) and the future (n=61), then each group was divided into episodic future thinking group and none episodic future thinking group. Two factors analysis of variance were conducted for the data which the type of time perspective trait is one independent variable as the between-subjects factor measured by the Zimbardo Time Perspective Inventory, and episodic future thinking level is another independent variable as a between subjects factor, which is operated by episodic future thinking task. The dependent variable is an indicator called D value that was computed by response time. The result showed that: (1) the main effect was significant on the time perspective traits that the implicit preference of healthy behavior choices of the middle school students with the trait of future time perspective higher than that of the middle school students with the trait of present-hedonistic and present-fatalistic time perspective. (2) The main effect of episodic future thinking level was significant that the implicit preference of healthy behavior choices of episodic future thinking group was significantly higher than that of the none episodic future thinking group. (3) Time perspective type and episodic future thinking level have an interaction effect on implicit preference of healthy behavior choice. It was suggested that episodic future thinking level plays a moderating role in the relationship between time perspective type and implicit preference of healthy behavior choice. Simple effect test results found that episodic future thinking significantly influenced the implicit preferences of healthy behavior choice in middle school students with present-hedonistic and future time perspective traits. However, it was not found the significant influence of episodic future thinking on the implicit preference of healthy behavior choice in middle school students with present-fatalistic time perspective. The findings of this study indicated that middle school students with future time perspective trait were more likely to choose positive health behaviors, and episodic future thinking could significantly promote the implicit preference of healthy behavior choice in middle school students with present-hedonistic and future time perspective traits.