Scientific creativity is considered as one of the essential traits required for future human resources, and tremendous research has been performed to enhance it. At this point, it is necessary to define variables that affect scientific creativity and understand their relationship. The purpose of this study is to represent the relationships among the variables related to scientific creativity as a structural equation model, and investigate the significance of path coefficients and goodness of fit indices in the model. Based on the analysis of previous studies, cognitive, affective, and environmental factors were chosen as latent variables affecting scientific creativity, and direct and indirect effects among variables were tested. A scientific creativity test, scientific affective test, family environment test, GALT(Group assessment of logical thinking), and scientific knowledge test were implemented. Two hundred and nine students' answers were analyzed. The results are as follows: Cognitive and environmental factors have a significant direct effect on scientific creativity. Affective factor didn't show direct effect on scientific creativity. However, the mediation effects of affective factor were shown in the relationship between the cognitive factor and scientific creativity. This research has significance in that overall relations among the variables related to scientific creativity were derived. Educational implications were discussed based on the results.