This paper explores the program of theology of science proposed by renowned Polish physicist and philosopher, Michael Heller, with a particular focus on its ontological dimensions through the lens of Trinitarian theology. Firstly, an overview of the status and current discussions of theology of science is presented. Next, drawing on Heller's key texts the Trinitarian doctrine is used to enhance the intelligibility of the Universe, wherein the dynamic interplay of unity, diversity, and relationality is mirrored in the structure of physical reality itself. Most importantly, however, we examine how Heller's theological perspective thus equipped provides justification for the specificity of the method of science itself, thereby revealing new dimensions of relations between science and theology. Through critical engagement with Heller's thought, this paper seeks ultimately to illuminate the profound implications of a Trinitarian perspective in his theology of science, shedding light on the interconnectedness of Christian doctrine and ontology in shaping our understanding of the universe and its underlying structure.