Aims: The purpose of the article is to harmonize the philosophical, educational, and philosophical-scientific aspects of teaching natural science at different educational levels. The educational and pedagogical system functions as a complex of interconnected elements of methodological, organizational, and ideological nature. Each of these segments (especially teaching and methodological activities) needs to be correlated to achieve the integrity of the educational paradigm, in which natural science knowledge forms its own principles and interacts with humanitarian or applied knowledge. The task of the research is to highlight the peculiarities of the formation of thinking activity in students of educational levels. Methodology: The methodological arsenal used in the study combines general scientific, scientific and educational, and philosophical clusters. The methodological approaches used to examine the peculiarities of teaching natural sciences through the prism of philosophy have a dialectical and synergistic basis. The complex of multidisciplinarity and pluralistic-oriented methodology is identified as a promising area of research, which makes it possible to consider natural science not as a separate (or even isolated) component of science and education, but to combine it with information technology and humanitarian and worldview elements of the world picture. Results: The results of the study indicate the formation of new benchmarks for the quality of science education in modern pedagogy and science. The key achievement of modern education is the reorientation from the fragmentation of knowledge to its synergistic integrity. The practical and pedagogical value of this process is to form the foundations of subject-action and visual-figurative thinking. Scientific Novelty: The scientific novelty of the study is focused on building educational strategies in which natural science knowledge forms synergistic links with applied and humanitarian knowledge, ensuring the integrity of fundamental and flexible skills and the universality of thinking activity. Conclusion: Natural science remains a fundamental component of the educational system, forming an adequate understanding of the existential dimensions of human existence. At the same time, modern education offers a new approach to the organization of knowledge and skills of students at different levels, which involves the study of the laws of the universe, nature, society, human, technology exclusively in an interdisciplinary complex dimension.