As one of the representative emerging architects in Japan, Junya Ishigami has further advanced the redefinition of the relationship between architecture and nature within the lineage of Japanese modern architecture characterized by “lightness, delicacy, and closeness to nature,” presenting a spatial characteristic that can be summarized as “transparency.” So-called “transparency” refers to the morphological diversity, formal innovativeness, and layered superimposition of architectural space; through the dissolution of boundaries, the adjustment of scale, the use of light-transmitting materials, and the incorporation of the natural environment, architecture is able to clearly manifest characteristics of spatial openness, formal multiplicity, and rich stratification. The purpose of this study is to analyze the characteristics of transparency that appear in Junya Ishigami’s architectural spaces, to elucidate the essence of his transparency, and thereby to explore the expression and application of transparency theory in contemporary architectural design. This study applies the theory of transparency in architecture to examine Junya Ishigami’s architectural cases, and summarizes the manifestations of this characteristic as: the collectivity of internal and external spatial assemblages, the freedom of structural organization, and the superimposition of perception and form. It identifies the possibilities of transparency theory within modern architectural space and demonstrates the characteristics of transparency embodied in Junya Ishigami’s architectural spaces. These findings indicate that transparency theory has the potential for broader application in future architectural design.