Background: The results of the Programme for International Student Assessment (PISA) 2012 showed that Indonesia, Malaysia, and Thailand underperformed and were positioned in the bottom third out of 65 participating countries for mathematics, science, and reading literacies. The wide gap between these three countries and the top performing countries has prompted this study to examine the influence of students' affective characteristics on their performance in mathematics literacy using a multilevel analysis. The purpose of this study is to examine the relationships among affective characteristics-related variables at the student level, the aggregated school-level variables, and mathematics performance by using the Programme for International Student Assessment (PISA) 2012 dataset. Method: The data used for the analysis were retrieved from the official PISA website. The student samples from Indonesia, Malaysia and Thailand were 5, 622, 5, 192 and 6, 602, respectively. The data were analysed using descriptive statistics, and a hierarchical linear modeling (HLM) approach with the HLM version 7.0 computer programme. Results:Different patterns of relationships were found between student- and school-level variables and mathematics performance in the three countries. The common student-level variable is attitudes towards learning outcomes, which predicted an increase in scores for the Indonesian, Malaysian, and Thai models. At the student level, the strongest predictor on mathematics literacy performance was mathematics self-efficacy for both Indonesian and Malaysian models, and perseverance for the Thai Model. At the school level, school average mathematics self-efficacy was the strongest predictor of mathematics performance in the Indonesian model; average openness to problem-solving in the Thai model; and school average instrumental motivation, mathematics behaviour, and attitudes towards learning outcomes predicted a decrease in scores for the Malaysian model. Conclusion: The inconclusive results of the multilevel analysis has demonstrated some interesting points for discussion, though the results could be attributed to the differences in education system and a diversity of cultural context in each individual country. This study contributes to providing evidence-based policy making in addition to informing the mathematics teachers the particular students' affective characteristics, which should be strengthened to ensure better mathematics learning outcomes in Indonesia, Malaysia, and Thailand. Implications of the findings and limitations are discussed.