The philosophy of Islamic education is to produce good individuals, believers and be devoted servant aligned with the goal of human beings creation based on the revelation of the Quran and hadith. The success of this philosophy is dependent on the curriculum implementation focusing on understanding, mastering and applying knowledge integrated well with thinking skills. Nowadays, the education system is more concentrated on teaching students how to use thinking skills, solve problems and making a decision. The implementation of higher level thinking skills has been implemented in schools and received positive and negative feedback from many people, especially from teachers and students. From previous study, more research has been focused on teacher issues than students' on higher order thinking skills. Based on this point, this study aims to investigate the level of understanding, mastering and the problems faced by the students in answering higher order thinking skills ( HOTS) questions. The design of this study used mixed method approach. A total of 138 students were involved in this study. Data was obtained from three instruments which is a set of HOTS questions, questionnaire and interview. The hierarchy of Taxonomy Bloom applied in this study is understanding, application and analysis. The data was analysed using statistical package for social science analysis. The findings show the level of students understanding and skills in answering HOTS questions is weak. It shows that high order thinking skills (HOTS) questions are still not mastered by the students. The results from data analysis can be used as a guideline in helping the students to learn in higher order thinking skills questions. Besides that, the implications and recommendations can give benefit to ministries, schools, teachers, scholars, policymakers and the community in improving the level of teaching practices based on higher order thinking skills (HOTS) as envisaged in the Education Development Plan 2013-2025.