Nowadays promoting equity is one of the fundamental values of China's educational policies. However, the issue of gender equity, especially gender differences in education, is still overlooked by national policies and school education, particularly for the group of floating children in urban primary schools. What is the status quo of the gender differences of floating children in schools today? Will the floating children influence the local classes in gender difference when they attend urban schools in megalopolis like Shanghai? And how? Does the group of floating children vary the same ways in gender difference as in social stratification? Is this gender difference relevant to the variation of school quality or school locations? Why is there the learning difference between boys and girls, etc? Based on the five dimensions of education quality by UNESCO (Learner, Environments, Content, Processes and Outcomes), we try to use learning process to explore and analyze the status quo of gender difference in Shanghai primary schools today, and then attempt to explain why the gender gap is so great in school education for the floating population in Shanghai urban primary schools. We selected ten primary schools in four different districts in Shanghai. Some schools are located in the city center, while others in the outskirt. We interviewed 55 teachers (including 36 female teachers and 19 male teachers) and conducted class observations (100 lessons in all) in seven schools. In the process of data collection, using NVivo 9 and with the interviewees' permission, we recorded, decoded and analyzed all the data. Our findings show that the participation of floating children has influenced the local classes, especially on gender percentage in the schools and classes which more floating children attend. The percentage of the boys is bigger than that of the girls, especially for the families of floating workers. Also, the gender divide between boys and girls is big, as is reflected in student performance in class, teacher-student relationship, etc. When we try to explain the differences, we find that the traditional and patriarchal thought is still popular, especially in the families of floating children today. This patriarchal culture has solidified the social division of gender role first in family, then in school education it is reinforced and even reproduced through teacher-student interaction in the classroom. Thereby the processes of education seem to have widened the gender differences and even gender gap in terms of students' classroom behavior and academic performance. Finally, we suggest some solutions to narrow the gap, such as raising the parents' awareness of their children's education, strengthing the home-school collaborations, as well as effective measures taken by schools.