In this paper, we analyze recently collected data that conducts a unique assessment of high school student performance for over two thousand students from five Chinese provinces. Across three domains of scientific intelligence tested, we document heterogeneous gender gaps in academic performance. These differences generally arise due to differential productivity of inputs to the education production process and not differential levels of inputs. At many quantiles of the achievement distribution, girls perform better than boys when identifying scientific issues, whereas the converse holds on the portion of the assessment that measures whether one can apply scientific evidence. These differences may partially explain the subsequent gap in decision to major in specific STEM disciplines in college. Further, our results imply caution from using a single summative gender achievement gap measure when gender gaps in subject knowledge are not constant across each domain of intelligence examined within the test.