This study explored the ecological characteristics and maintaining factors of Taiwan’s school refusal issues from the viewpoint of ecological systems, examining individual, family, and school aspects. An exploratory sequential mixed method research design was utilized in this study. First, qualitative interviews were conducted with four guidance teachers from Taiwan’s junior high schools. The qualitative data were analyzed using the categorical-content method to explore the ecological characteristics of school refusal phenomenon through individual, family, and school aspects. Thereafter, on the basis of the qualitative analysis results, a questionnaire was developed and administered among 239 guidance teachers from Taiwanese primary, junior high, and high schools. Descriptive statistics and principal component analysis were applied to analyze the quantitative data. The qualitative results highlighted the following ecological characteristics of Taiwan’s school refusal phenomenon: (1) the individual aspects entailed internal emotional states, external behaviors, physical symptoms, and need for psychological medication or special education; (2) the family aspects comprised relationship between parents, family relationships and expectations, parenting styles and regulations, and economic status and resources; and (3) the school aspect constituted student learning conditions, relationships with teachers, relationships with peers, and rules of a school system. The quantitative research results indicated the following ecological characteristics index of school refusal: (1) personal anxious avoidance, (2) familial overprotection and conflicts, (3) personal and familial over-expectations, (4) personal opposition and indolence, (5) inactivity and lack of motivation, and (6) school pressure and personal physical discomfort. Moreover, the quantitative research results demonstrated that the maintaining factors index of school refusal comprised the following: (1) class management challenges, (2) problems with cooperation within school system, (3) issues of personal daily routine and Internet management, (4) family anxiety toward school systems, (5) insufficient parental intervention against attacks from child, and (6) family lacking knowledge on school refusal. Finally, the results were discussed in more details and provided suggestions for practice and further studies.