This study examines the gender gaps in mathematics and physics in Chinese middle schools. The data is from the Education Bureau management database which includes all middle school students who took high school entrance exam in a district of Beijing from 2006-2013. The ordinary least square model and quantile regression model are applied. This study consistently shows that the gender gap is unfavorable toward female students in mathematics and physics while favorable toward female students in Chinese and English. Gender gaps favoring males in math and physics become more noticeable among the students who receive the top tier scores in math and physics testing. However, females' students' advantage in Chinese and English decreases along the distribution from the bottom to the top percentiles. There are significant intersections between rural residency and gender. Rural students (regardless of gender) perform less well than urban students in all subjects and rural female student show the worst testing scores compared with the other subgroups in mathematics and physics.