Complex thinking competency enhances the high cognitive capacities necessary for the future of education. This study aimed to analyze these capacities through its sub-competencies (critical, systemic, and scientific thinking). We worked with the Cross Industry Standard Process for Data Mining methodology, with an original database of class data of 33,319 unique students, 46 different variables, and a random identification number. The variables were sociodemographic information, academic information, subject admission, competencies, and activities. Statistical analyses identified correlations between competency and sub-competencies. The findings show that (1) critical thinking is strategic in the development of complex thinking and its sub-competencies; (2) Development of Critical Thinking skills early in the curriculum can lead to a cascade effect, enhancing competence and sub-competence development; and (3) an overall performance encompasses the semester results. The study is of value to the academic, technological, and social communities to provide opportunities for the design and implementation of challenging scenarios for the future of education.