Education enrollment and attainment rate in the primary and secondary education stage in China have reached a comparatively high level but the education quality gap between rural and urban students still remains. Based on the cultural deprivation theory, this research explores the reasons for students’ academic performances and cognitive capability differences based on their household registration type, rural or urban, taking into account student, family and parents, teacher and school characteristics. By using an extensive panel data set drawn from the China Education Panel Survey (2013-2014) (CEPS), this research employs Ordinary Least Squares (OLS) method and multiple regressions to unveil the causes of rural-urban education gap during junior high school. The household registration system limits the education choices of rural students whilst urban students are gaining accumulative benefits from it. This study found that urban students outperform rural students on both academic results, namely Chinese, English, and math, and cognitive ability. The major reason lies on students’ family background, parents’ education level and their involvement in education.