The purpose of this study is to probe into the effect of metacognitive thinking strategies with different teaching strategies in an online inquiry-based junior high course. Two types of teaching strategies were applied in classes with totally 69 students of 9th graders in New Taipei City. Among participants, 34 students were in the experimental group accepting the strategy of "Collaborative Online Inquiry" while the control group of 35 students with "Personal-based Online Inquiry". Data were collected for a six-week lesson on this topic "Campus Folk Song". ANCOVA and class observations, instructors' diary, and interviews with students are measured to understand the different effects of two teaching strategies on students' metacognitive thinking strategies. The result shows that students by "collaborative online inquiry" in experimental group perform their metacognitive strategies better than those by "Personal-based Online Inquiry" in the control group. [For the full proceedings, see ED562127.]