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 < 0.001, Cohen's d = 0.301), and outperformed girls in multiple-choice items. Our study also highlighted that boys were likely to outperform in the higher score ranges, as well as lower score ranges. Finally, we also found that the boys had significantly greater variabilities in science achievement and interest (variance ratio [VR] >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.