In this study, we explored the gender differences in science achievement, interest, creativity, and so on, using a national representative sample from the National Assessment of Education Quality (NAEQ). NAEQ assessed the Grade-4 (n = 112,314) and Grade-8 (n = 74,808) students’ scientific literacy of Mainland China in 2017. The findings indicated that there was no gender difference of science academic achievement in both Grade 4 and Grade 8 in China. However, scientific interests varied in different grades and disciplines. Girls had a higher interest in science in Grade 4 and higher interest in biology in Grade 8. The 8th-grade boys had much higher creativity than girls (p 1.1), while the girls had slight greater variability in creativity (0.9 < VR <1.0). Our results provide a reliable Chinese evidence for international studies on gender differences. However, further research is demanded to study the reasons behind gender differences deeply.