A major concern in science education is how to help students form science identity to increase their aspiration for STEM careers. Given the key role of experiences in individual’s science identity formation, STEM experiences related to project-based learning (PBL) have received increasing attention in recent years. The purpose of this study was to examine how high school students’ science identity has been affected by the multi-dimensional STEM-PBL experiences, i.e., scientific inquiry, technological application, engineering design, and mathematics processing. Employing two independent questionnaires, we quantitatively investigated the correlation between multi-dimensional STEM-PBL experiences and science identity with 400 high school students (grades 7–12) from a range of public schools in China. Results indicated that the level of students’ engineering design experiences was the lowest compared to the other three dimensions. Regression analysis revealed that three dimensions of STEM experiences, scientific inquiry, technological application, and mathematics processing, were significant and positive predictors of science identity. Engineering design experiences, however, failed to predict science identity.