The Scientific Metastructure Theory is a novel conceptual framework that unveils the intricate interplay temporal selection process across diverse scales and systems within the universe, explaining its metastructure scientifically. This theory redefines life as a dynamic process wherein biological and artificial machines actively contribute to universal entropy increase through the consumption and re-consumption of energy and matter. Through iterative consumption and accumulation, these machines gain complexity, efficiency, and adaptability. The temporal selection process emerges as a driving force, favoring complex machines capable of maximizing resource acquisition, driving increase in universal entropy. This selection process operates universally, shaping not only biological evolution but also atomic and chemical interactions, technological advancements, societal structures, and even religious systems. Also presenting a mathematical framework, this paper provides a structured understanding of how biological and artificial machines contribute to entropy increase through compounded complexity-driven temporal selection. Through diverse examples, the framework is illustrated across scales, offering a unified perspective on the scientific metastructure of reality.