This study aims to explore the relationship between religion and science of Isaac Newton with focusing on his concept of God. The general understanding of Newton is a 'scientist' Newton who completed the Scientific Revolution. When we consider the life and works of Newton, however, the received picture of Newton, which was constructed from a contemporary scientific perspective, reflects only a part of the broad enterprise of Newton. His intellectual project covers from science, via theology and religion, to alchemy. Examining the current understanding of Newton critically, the writer insists that Newton's thought should be investigated from the contemporary concern of the Newtonian period, which pursued 'the unity of Truth.' The core of Newton's thought is not science but religion, especially the concept of God, 'the Lord God of Dominion.' What Newton looked for is 'the unity of truth,' which is 'the unity of knowledge about God.' 'The Lord God of dominion,' as an intelligent Agent, created the universe, imposed natural laws into it, and preserves and cares it. While Newton's scientific enterprise deals with the structure of created world and its natural laws, through observation, experiment, and induction, Newton's theological project investigates prophecy to decode the special providence of God, which occurred and will occur in human history. For Newton, 'the book of Nature' and 'the book of Bible' are not conflict but complementary. The religion and science both are constructing factors of a holy alliance and make a single epistemic discourse. To achieve the goal of the study, this article consists of three main chapters. Chapter Two critically discusses different understanding of Newton, scientist, theologian, or alchemist. The third chapter investigates Newton's concept of God, the Lord God of dominion. The forth chapter explores the relationship between religion and science of Newton. The Chapter Five as a conclusion presents a summary and evaluation.