Creativity is an important skill in the 21st century, and design thinking has been proposed as a methodology for fostering creativity. Design creativity involves two non-rational aspects: motivation and empathy. However, little is known about how empathy and motivation work in synergy with creativity. This study explored the underlying mechanisms of empathy and motivation in creativity in design thinking. We built an explanatory model to examine the effect of empathy on motivation and creativity and the mediating effects of four aspects of motivation (i.e., attention, relevance, confidence, and satisfaction). In the study, 220 6th-grade students participated in an integrated STEM curriculum that centered on design thinking activities that lasted one semester, and then completed a questionnaire measuring their perceptions of empathy, motivation, and creativity at the end of the design activities. Partial least squares structural equation modelling was used to analyze the collected data. The results showed that empathy positively predicted creativity. In addition, empathy had a significant impact on creativity through the effect of intrinsic motivation, but not through that of extrinsic motivation. Among the four aspects of motivation, attention, relevance, and confidence each strengthened the association between empathy and creativity. However, satisfaction had a negative effect on creativity and a non-significant mediating effect. These findings increase our understanding of the internal mechanisms of design thinking and creativity. Some practical implications of empathy and motivation in creativity are also discussed.