Meta-subject competencies, such as self-organization and self-regulation of student learning, are becoming key in modern education. The aim of this study was to model the student learning process and its components. A comparative analysis of the concepts of self-organization and self-regulation, identifying their similarities and differences in key aspects, was conducted within the framework of the research topic. A survey of students in Omsk and Bishkek was conducted to develop the models. Respondents’ rights were protected by the anonymity of the survey procedure. A cognitive Student Learning Activity Model was developed using a cognitive approach. This cognitive approach incorporated expert methods, graph theory, and other methods. An analysis of scientific data showed that self-organization creates a framework for learning activity. Self-regulation, in turn, ensures the subject’s cognitive activity within this framework. This approach allows students to flexibly respond to emerging difficulties. Student self-assessments of selforganization differ by 6–7% between the samples of Russian and Kyrgyz students. These differences may be due to differences in mentalities and educational systems. The results of the simplicial analysis revealed that the implicit factors influencing student learning are the “assessment” and “control” factors of educational procedures. These factors are elements of self-regulation of learning. The simplices with the largest number of elements, the “psychological maturity” and “reflection” factors of the student, are also elements of selfregulation of learning. Experts advise educators to consider these factors in educational activities and the rationale for management decisions.