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Analytical thinking skills are critical thinking skills and higher-order thinking skills that meet students’ demands in the 21st century. This study aims to analyze the student’s analytical thinking skills in the natural sciences, particularly in new and renewable energy. This study was a sequential explanatory design with quantitative and qualitative methods. Data was obtained from the interview, observation, and essay test to students of the Madrasah Ibtidaiyah Teacher Education Program Study at IAIN Surakarta (Indonesia) to determine a characteristic of the students’ analytical thinking skills. The results showed that the mean scores of the pre-test, post-test, and effect size were 54.34, 74.91, and 2.91, respectively. These results revealed that analytical thinking skills in the concept of new and renewable energy in the experimental group were higher than the control group. Innovative learning like PBL had a potential as the alternative method to increase the analytical thinking skills of student. These findings were expected to provide a general characteristic to lecturers and researchers on the students’ analytical thinking skills in higher education in the natural sciences, particularly in the concept of new and renewable energy by implementing the Problem Based Learning (PBL) model.