Students with low family socioeconomic status (SES) often have lower academic achievement than their peers with high family SES, as has been widely demonstrated. Nevertheless, there is a group of students beating the odds and achieving academic excellence despite the socio-economic background of their families. The students who have the capacity to overcome adversities and achieve successful educational achievements are referred to as academically resilient students. This study’s purpose was to identify the protective factors among academically resilient students. A total of 46,089 students from 303 primary schools in grade 6, 55,477 students from 256 junior high schools in grade 9, and 37,856 students from 66 high schools in grade 11 in a city in northeast China participated in the large-scale investigation. Students completed a structured questionnaire to report their demographic information, psychological characteristics, and three academic tests. A causal comparative research model was applied to determine significant protective factors associated with resilient students (referring to students are resilient if they are among the 25% most socio-economically disadvantaged students in their city but are able to achieve the top 25% or above in all three academic domains). Multivariable logistic regression analyses found that the intrinsic protective factors for resilient students included higher proportion of academic importance identity, higher proportion of achievement approaching motivation, longer-term future educational expectation, and more positive academic emotion compared with non-resilient students; the extrinsic protective factors included parents’ higher proportion of positive expectations for their children’ future development, as well as more harmonious peer and teacher–student relationships. The results of this study provide important targets for psychological intervention of disadvantaged students, and future intervention studies can increase their likelihood of becoming resilient students by improving their recognition of the importance of learning, stronger motivation for achievement approaching, longer-term expectations for future academic careers, and positive academic emotions and harmonious teacher–student relationships.