This study aimed to analyze the critical thinking skills of students in learning of environmental change material using e-learning madrasah. This study used explanatory sequential design by mixed-methods experiment. The data were collected by interviewing, observing, and essay testing that have indicators modified from critical thinking skills by Watson-Glaser, Facione, and Ennis. There were 67 participants in this study as 7th grade student at a junior high school in Sleman district. Quantitative data analyzed by determining average score and standard deviations and, qualitative data analyzed from interviews and observation. Quantitative analysis showed that there were 3 levels of student's critical thinking skills which were 14 students (20.90%) in the high category, 38 students (56.72%) in the middle category, and 15 students (22.38%) in the low category. Qualitative analysis indicated learning model made students to learn actively, independently, and enthusiastically looking for several sources. This study provided information about student critical thinking skills in junior high school, especially in the environmental change matter which are still low. Thus, the alternative learning strategies to improve students critical thinking skills are very needed. Besides, information on the application of the discovery learning model with e-learning Islamic school was obtained in the COVID-19 pandemic.