This study aims to investigate the effect of inquiry-based learning and direct instruction in enhancing mathematical thinking abilities among secondary school students to examine students' attitudes towards inquiry-based learning as a method for improving mathematical thinking abilities. This study adopted the quantitative research method. Eighty-six questionnaires were issued, and 86 were valid, with a validity of 83.5%. The mathematical thinking ability test consists of pre-test and post-test items. There are 43 students from Class 1--control group and 43 students from Class 2--experiment group, Grade 3. This study finds that the achievements of inquiry-based learning are better than direct instruction in improving secondary school students' mathematical thinking abilities; students who learn with inquiry-based learning to improve secondary school students' mathematical thinking abilities have a high level of satisfaction. Based on the analysis results, the following suggestions have been put forward. Teachers should cultivate students' confidence and abilities by guiding more active discussions and cooperation. Teachers should cultivate students' patience and strategic awareness in problem-solving. This teaching method's success relies on teacher guidance, an open classroom atmosphere, and active interaction among students.