Enhancing students' analytical thinking skills holds great promise for bolstering a nation's economic growth, fostering a dynamic learning culture, and nurturing human capital development. It is especially critical in today's rapidly changing landscape, where the demand for skilled, adaptable graduates is high. Achieving and sustaining these skills hinges on individuals' awareness of their own thinking processes. Thus, this study aims to investigate the relationship between metacognitive knowledge and analytical thinking among university students in Malaysia. Besides, it assesses the impact of metacognitive regulation and control on analytical thinking. Data was gathered by administering web-based questionnaires to students enrolled in two public universities and two private universities situated in Malaysia's central region. Employing convenience sampling, a total of 184 respondents participated in the survey, responding to 5-point Likert scale questionnaires designed to gauge metacognition (both knowledge and regulation) and analytical thinking. The data analysis was conducted using Partial Least Squares Structural Equation Modelling (PLS-SEM), a technique chosen for its suitability to handle complex relationships within the study variables. PLS-SEM, coupled with the bootstrapping method, was employed to ensure a robust examination of the interactions among metacognitive factors and analytical thinking. The use of the bootstrapping method enhances the reliability of the results by generating multiple resamples and assessing the stability and significance of the model parameters. The results revealed a significant relationship (p < 0.01) between metacognitive knowledge and analytical thinking, with knowledge of persons and knowledge of strategies proving to be influential in enhancing analytical thinking abilities with the correlation coefficients (R-values) of 3.528 and 3.815, respectively. In terms of metacognitive regulation, this study identified a noteworthy positive impact, highlighting the role of metacognitive regulation and control in bolstering analytical thinking with an R-value of 2.985. These findings have far-reaching implications for educators, offering valuable guidance on empowering university students to become more self-reliant and efficient learners by imparting skills in planning, monitoring, and self-assessment of their learning processes for improved academic performance within the university environment. This, in turn, has the potential to yield improved academic performance, particularly the development of analytic thinking and offers educators the opportunity to craft more effective instructional materials and activities tailored to harness the power of metacognition in education.