The enactment of the revised School Places Allocation Systems at the compulsory stage in 2004 had the aim of desegregating Hong Kong's non-Chinese linguistic minority (NCLM) students by including them into ethnic Chinese-dominated mainstream primary and secondary schools. Because of the presumed cause-consequence relationship between desegregated school participation and academic achievement, in specific second language Chinese (CSL) acquisition, the challenges that such students face in participating in mainstream education and learning Chinese, no doubt, deserve to be examined. This qualitative study conducted in-depth interviews with 18 secondary students of South Asian/Southeast Asian minority backgrounds enrolled in mainstream schools. Drawing on both cultural and institutional paradigms of explanation for educational achievement, we argue that the reasons inhibiting the minority students' academic involvement are not simply their linguistic challenges but also the institutional constraints in the mainstream education system unique to this population. This study calls for a shift in school desegregation arrangement from one focusing narrowly on physical desegregation to a more comprehensive set of policies that embrace the institutional factors including teacher expectation, resource availability, and bilingual support, crucial to reduce racial differences in achievement.