The digital information age requires skills and strategies that are crucial in comprehending online academic texts. Also, research has emphasized the crucial role of critical thinking (CT) in education. Thus, this explanatory sequential mixed-methods study aimed to (a) identify Iranian EFL students’ metacognitive online reading strategies and CT skills, and (b) investigate the possible relationship between Iranian EFL students’ metacognitive online reading strategies in academic texts with their CT skills. To these ends, 80 Iranian EFL university students, selected nonrandomly from Shahrekord University, took part in this study and responded to the Pookcharoen’s (2009) Online Survey of Reading Strategies and Facione, Facione, Blohm, and Giancarlo’s (2002) California Critical Thinking Skills Test. In the follow-up, to probe into metacognitive online reading strategy use, 10 Iranian EFL university students were selected to do think-aloud online reading tasks. The descriptive statistics indicated that the EFL university students greatly preferred to use problem solving strategies more, followed by different global and support reading strategies respectively. Also, evaluation and inductive (sub)skills of CT were used mostly by the university students. Moreover, the results of the think-aloud provided evidence in support of quantitative results, confirming various problem solving, global and support strategy use in online academic reading. Furthermore, Pearson correlations revealed a positive and significant relationship, though it was small, between metacognitive online reading strategy use and CT skills. Integrating the findings from the quantitative and qualitative components call for metacognitive strategy assistance and instruction and CT development to improve online reading comprehension.