The development of Higher Order Thinking Skills (HOTS) is a key objective in 21st-century mathematics education; however, students’ ability to engage in higher-level cognitive processes remains relatively low. This study aims to investigate the role of bilingual instruction in promoting HOTS in mathematics learning at the junior high school level. A mixed-methods approach with an explanatory sequential design was employed. The quantitative phase used a quasi-experimental design involving an experimental group receiving bilingual instruction and a control group receiving conventional instruction, while the qualitative phase explored students’ cognitive processes through observations and interviews. The results revealed that students in the bilingual instruction group achieved significantly higher HOTS scores compared to those in the control group, as indicated by the post-test mean difference and a statistically significant result (p < 0.05). The N-gain analysis also showed moderate to high improvement in the experimental group, while the control group demonstrated lower gains. Qualitative findings further indicated that bilingual instruction enhanced students’ conceptual understanding, cognitive engagement, and metacognitive awareness, although initial challenges related to language proficiency were observed. These findings suggest that bilingual instruction is an effective pedagogical approach for fostering higher-order thinking in mathematics learning. The study contributes to the field by providing empirical evidence on the integration of language and content learning to support cognitive development.