Background Blended learning in DESEC only started after the introduction of the internet in recent 5 years. However, there is still no research paying attention to this region, because the area is remote and research subjects are not easily accessible. This article has potential application value in helping the government and educational institutions to make decisions on blended learning strategies supporting poverty alleviation through education in poor and remote areas and ethnic region. The study will be the first to examine satisfaction and continuance intention of blended learning in the DESEC. Objective To identify junior high students’ perception of satisfaction and continuance intention for blended learning in DESEC. To identify the strongest factors affecting junior high students’ satisfaction and continuance intention of blended learning in DESEC. Methods A subsample of 635 junior high students participated online survey with consent of their parents verbally in computer room in schools under teacher’s instruction. Data was coded and analyzed to generate descriptive statistics and inferential statistics. Structural equation model was used to evaluate the model of satisfaction and continuance intention of blended learning. Results The level for evaluating students’ agreement on each of item were interpreted “agree” (3.76–3.89). The model explained variances (R2) of Continuance Intention, Satisfaction and Perceived usefulness were 0.665,0.766,0.718 respectively. Information quality, self-efficacy and confirmation directly and indirectly contribute to junior high students’ satisfaction with blended learning, which further confirmed their continuance intention of blended learning. Conclusion Information quality was the strongest factor affecting the junior high students’ continuance intention of using blended learning, while confirmation was the strongest factor affecting the junior high students’ satisfaction of using blended learning in DESEC. Junior high students do not have a strong and distinct perception on satisfaction and continuance intention for blended learning in DESEC.