To improve and continue educational sustainability development, we expect to understand the learning problems of disadvantaged students for sustainability in rural areas. This study collected an integrated dataset, including 16 features with 883 records, from an elementary school in a rural area in Taiwan. Then, this paper proposes an integrated features selection method to integrate four different feature selection methods for finding the key features of academic achievement, and utilizes a statistical test to explore the differences in various student backgrounds in the nine key features and the graduated score. The statistical test shows that between the ordinary students and disadvantaged students, there were differences in the key features and the graduated score, and this paper also found that the five groups of disadvantaged students exhibit differences in academic achievements. To determine these differences, this study carried out interviews on six different students’ identity backgrounds, and the majority consensus of six groups of students was summarized as personal, family, and school aspects. The results show that there were many learning problems in this rural elementary school: (1) the education levels of most of the parents (72.3%) were below the college level; (2) 73% of parents were staff members and workers; (3) 26.4% of students in the school were disadvantaged; and (4) the age range of student’s parents was from 30 to 64 years. For the sustainable education of rural areas, this study suggests that the educational management must invest greater resources and make more effective policies a priority for teachers in rural areas and that teachers must pay more attention to aboriginal students in terms of learning motivation and must actively interact with their parents.