This article began from a classical problem that the concept of “religion” cannot be easily defined, and then attempted to obtain the clue from the “religious consciousness”, as an approach to study the religious phenomenon from the perspective of cognitive science. It means that the religion cannot be understood only from its surface structure. It is a major premise of this article that the people's religious consciousness must be taken into account, for the substance of their religion appears. Especially, the natural religion of Japan and Bali where the structure and conflict of people's religious consciousness has high complexities was treated as the case study. There are two points of conclusion obtained from such consideration. The first point is that the religious consciousness occurs in general because of the mechanism of reflexive religious consciousness. It is an argument that this mechanism consist of the following three elements, i.e. “intuitive religious reality”, “generation of religious meaning”, and “denotative religious consciousness”. The second point is that, looking from a reflexive religious consciousness, the religion exists as “sacred system of life”. It is an attempt to capture the religion from its structure of consciousness and existence.