Natural Science is a learning related to everything around us. One of the subject matter in natural science is the motion system that often occurs in daily life. However, some of the students have misconceptions about the motion system. It required the critical thinking skills of the students in understanding the concept to resolve a problem in society. Critical thinking skills is one of the skills that must be possessed by students because of the demands in the 2013 curriculum. Critical thinking skills can be influenced by several factors, one of them is students’ learning style. This study aimed to analyze the critical thinking skills of junior high school on natural sciences based on the differences in learning styles. This study took sample of students in the first, second and third grade of junior high school. In this research, the researcher uses descriptive method. To analyze the data, the researcher used mix methods (qualitative and quantitative). The technique of collecting data uses observation and tests. Observation is used to find out the types of the students’ learning styles, while tests to measure student’s critical thinking skills. The results showed that there were verbal-linguistic learning style (73.0%), logic-mathematic (67.6%), kinesthetic (60.0%), visual-spatial (60.2%), music (62.0%), and interpersonal (61.1%). So, the verbal-linguistic learning style was better than critical thinking skills.