The study aimed to identify the effect of using Metacognitive Strategies on critical thinking skills among students of the Islamic Science University of Malaysia. The quasi-experimental method was applied in the study. The respondents in the study consist of 52 students who were in first year of bachelor level at the Islamic Science University Malaysia for the first Semester, 2015/2016. They were selected purposively and distributed randomly into two groups; 26 students in experimental group and the other 26 students in control group. To achieve the purpose of the study, the researchers designed a teacher`s manual and student`s worksheets according to the Metacognitive Strategy. The data were collected using a research instruments: a pre and post test in Watson-Glaser's' Critical Test. The results of this study showed that there was also statistical significant difference between the groups in critical thinking skills, in favor of the experimental group. In light of these results, the study recommended that using of Metacognitive Strategies in teaching Arabic Reading should be expanded to other educational stages in Malaysia.