This research article explores the value foundations for developing independence in the sciences as a multi-level axiological system that determines the stability and depth of independent cognitive activity in mathematics, physics, chemistry, and related disciplines. When studying physics, mathematics, and engineering disciplines, value orientations act as an internal regulator, motivating students to formulate hypotheses, verify their own conclusions, and engage in intellectual inquiry. It has been established that epistemological values, including a pursuit of truth, respect for evidence, a willingness to reconsider positions in light of new data, as well as logical rigor and intellectual honesty, form the core that ensures genuine independence, not reducible to the formal completion of assignments. At the same time, it is emphasized that epistemological values – including the pursuit of truth, respect for proof, readiness to revise one’s positions in light of new data, as well as logical rigor and intellectual honesty – constitute the core that ensures genuine independence not reducible to the formal completion of assignments. Contemporary contradictions in the educational environment caused by digitalization manifest themselves in the fact that the availability of online resources, simulators, and databases creates technological conditions for autonomous learning; however, in the absence of stable value orientations, this frequently leads to superficial and fragmented assimilation of material and the replacement of independent work by the mechanical reproduction of algorithms, especially within the competence-based approach of educational standards. The following levels are distinguished: the ontological level of the value of exact knowledge as a means of comprehending the regularities of reality; the epistemological level, which emphasizes rationality, provability, and consistency; the praxeological level, associated with intellectual labor, perseverance, and mental discipline; and the pedagogical level, oriented toward recognition of the learner’s subjectivity, the right to error, intellectual search, and education as a process of personality self-transformation. The integration of these levels forms a holistic model of independence as a personal quality. The heterogeneity of value profiles is revealed, in which normative-ethical aspects of scientific honesty prevail over cognitive-activity orientations toward intellectual autonomy and persistence in problem solving. Differentiated interrelations are established between value orientations and manifestations of independence, including initiative in posing cognitive tasks, self-monitoring, readiness to overcome intellectual difficulties, and reflexivity in assessing results, with the dominant role belonging to the value-volitional complex that unites autonomy and perseverance. A typology of learners is presented that differs according to the configuration of value foundations, level of independence, and academic success. Groups identified include those with an autonomous-value, normative-adaptive, and externally motivated attitude toward the exact sciences, reflecting varying degrees of interiorization of values at the stages of school and higher education. Particular attention is paid to pedagogical factors of the educational environment, among which experience in research work, participation in scientific clubs and olympiads, regular solving of non-standard problems, and a dialogic style of interaction with the teacher exert the most significant influence on the formation of value foundations. These factors do so by creating conditions for experiencing authentic intellectual experience, cognitive conflict, and the appropriation of the values of exact knowledge.