<p>It is helpful to develop students’ view of the nature of science and further enhance their scientific literacy to let students fully recognize uncertainty in science learning. However, in science classrooms, the understanding of uncertainty is usually neglected. At present, there are relatively few studies on Chinese middle school students’ perception of uncertainty. Accordingly, this study established a theoretical framework of uncertainty (deficient, technical, scientific, consensus uncertainties). Then, using chemistry as the research context, we designed the questionnaires containing science reading texts for 560 Chinese grade 12 students. By guiding students to read the texts, we investigated their cognition and coping ways of the inherent uncertainty in science. The study found that, first, students’ perception of uncertainty was more sensitive and intense when they were faced with scientific, unfamiliar contexts where research conclusions have not yet been determined in the scientific community. Second, compared with the other three sources of uncertainty, the number of students who perceived the existence of technical uncertainty was the smallest and the perceived degree was the lowest. Third, students’ tolerance of uncertainty was above average in the face of uncertainty contexts, and there was a possibility of further improvement. Fourth, there was only a weak positive correlation between students’ overall perception of the sources of uncertainty and their intolerance of uncertainty. Based on the above research results, some suggestions were put forward to facilitate students to understand and cope with uncertainty in science learning.</p>